SAN FRANCISCO — The San Francisco 49ers sit alone atop the NFC West for now – hardly the kind of firm hold on the division they owned last October.

Alex Smith threw a 12-yard touchdown pass to Delanie Walker late in the third quarter and San Francisco held off the Seattle Seahawks 13-6 on Thursday night as the 49ers won their long-awaited division opener.

Frank Gore ran for 131 yards and the 49ers (5-2) took over sole possession of first place in the NFC West by making just enough plays to win this defense-first game, featuring two teams allowing fewer than 16 points per game.

Walker's score was San Francisco's first touchdown in seven quarters after an embarrassing 26-3 loss to the New York Giants on Sunday in a lopsided rematch of the NFC championship game. The tight end broke his jaw in two places at Seattle last Dec. 24 and sat out until the title game.

Smith went 14 of 23 for 140 yards in another subpar performance. The defense hung tough down the stretch.

NFC rushing leader Marshawn Lynch finished with 103 yards for Seattle (4-3).

It's now Jim Harbaugh 3, Pete Carroll 0 since these two coaching rivals started facing off in the NFL last year after all those memorable moments in the college game.

Harbaugh's teams sure have shown they are quick to forget their losses. The 49ers improved to 5-0 after regular-season defeats since reigning NFL Coach of the Year Harbaugh took over before last season.

Pulling off this one could give the 49ers some momentum, too. It was the first of two straight prime time games for San Francisco, which doesn't play again until Oct. 29 at Arizona.

The defensive fight left the animated coaches shaking their heads and hollering on opposite sidelines all game, offering plenty of entertainment for the sellout crowd of 69,732 at balmy Candlestick Park.

These teams met in Weeks 1 and 16 last season, with the 49ers beating Seattle 33-17 at home for Harbaugh's first victory as an NFL coach.

This one was close until the end.

After Walker's touchdown, Dashon Goldson intercepted a deep pass by Russell Wilson to thwart Seattle's next drive after NaVorro Bowman clobbered the rookie quarterback as he was trying to throw.

Smith gave the ball back with an interception of his own early in the fourth quarter. His fifth interception of the season matched his total from all of 2011.

Harbaugh went to backup Colin Kaepernick for one keeper play that lost a yard, Smith returned for third-and-goal on the 7. He scrambled to his left looking for an open receiver and Brandon Browner jumped in front of a pass intended for Randy Moss.

That gave Seattle the ball back with 11:58 remaining. Yet again, the Seahawks couldn't capitalize on a night of missed opportunities and dropped balls.

Gore had his third 100-yard game of the season, not to be outdone by Lynch on the other side.

Lynch carried 19 times and bounced back from a 41-yard outing in Sunday's comeback 24-23 home win against the Patriots. The 49ers and their top-ranked defense hadn't allowed a 100-yard rusher in 22 consecutive home games before New York's Ahmad Bradshaw ran for 116 yards and a touchdown Sunday – and now the Niners made it twice in five days.

Not that they should have been too surprised. This is Lynch, after all.

The last time they faced off, on Dec. 24, Lynch ran for 107 yards as San Francisco's defense had its streak of not allowing a 100-yard rusher end at 36 games. And his 4-yard touchdown run in the fourth quarter also was the first TD rushing allowed by San Francisco all season.

Wilson, who spoke leading up to the game that he couldn't wait for his introduction to this heated rivalry, went 9 of 23 for 122 yards, an interception and two sacks. Aldon Smith sacked him with 1:25 left, then Paul McQuistan was called for a chop block on Smith in the end zone with 43 seconds left. It would have been an automatic safety, but the 49ers declined the penalty. The play was reviewed and Seattle was short of the first down.

Wilson struggled four days after he threw two late touchdown passes as the Seahawks rallied for 14 points over the final 7:31 to stun New England on Sunday.

He had several deep balls in the first half that were right on target but the receivers couldn't come down with the football.

Another key miss helped seal it for San Francisco.

On Seattle's second-to-last drive, Patrick Willis tipped a pass by Wilson on third-and-12 just before the 2-minute warning.

San Francisco was in control of the division at this stage last season – sitting at 5-1 – but needed a big second half Thursday after a quick week of preparation to stay in first place.

Steven Hauschka kicked a 52-yard field goal as Seattle scored first for the seventh time in as many games this year. He added a 35-yarder early in the second quarter but missed wide left on a 51-yard try later in the quarter.

David Akers, who had eight of his NFL-record 44 field goals in the two games against the Seahawks last season, booted a 38-yarder late in the first quarter to make it 3-3.

Loading Slideshow...
  • Russell Wilson

    Seattle Seahawks quarterback Russell Wilson (3) sits on the bench during the fourth quarter of an NFL football game against the San Francisco 49ers in San Francisco, Thursday, Oct. 18, 2012. The 49ers won 13-6. (AP Photo/Tony Avelar)

  • Anthony Dixon

    San Francisco 49ers running back Anthony Dixon celebrates after their 13-6 win over the Seattle Seahawks in an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Alex Smith, Russell Wilson

    San Francisco 49ers quarterback Alex Smith (11) talks with Seattle Seahawks quarterback Russell Wilson (3) after an NFL football game in San Francisco, Thursday, Oct. 18, 2012. The 49ers won 13-6. (AP Photo/Ben Margot)

  • Steven Hauschka, Clint Gresham, Ben Obomanu

    Seattle Seahawks kicker Steven Hauschka (4), long snapper Clint Gresham (49) and wide receiver Ben Obomanu (87) sit on the bench during the second half of an NFL football game against the San Francisco 49ers in San Francisco, Thursday, Oct. 18, 2012. The 49ers won 13-6. (AP Photo/Tony Avelar)

  • Brandon Browner, Anthony Davis

    Seattle Seahawks cornerback Brandon Browner (39) runs past San Francisco 49ers offensive tackle Anthony Davis (76) after intercepting a pass by quarterback Alex Smith during the second half of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Tony Avelar)

  • Andy Lee, David Akers

    San Francisco 49ers place kicker David Akers (2) makes a field goal as punter Andy Lee (4) holds during the fourth quarter of an NFL football game against the Seattle Seahawks in San Francisco, Thursday, Oct. 18, 2012. The 49ers won 13-6. (AP Photo/Marcio Jose Sanchez)

  • Pete Carroll, Michael Robinson

    Seattle Seahawks head coach Pete Carroll walks next to fullback Michael Robinson (26) during the second half of an NFL football game against the San Francisco 49ers in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • NaVorro Bowman, Ray McDonald

    San Francisco 49ers linebacker NaVorro Bowman (53) and defensive tackle Ray McDonald (91) celebrate during the second half of an NFL football game against the Seattle Seahawks in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • Frank Gore, Clinton McDonald

    San Francisco 49ers running back Frank Gore (21) rushes past Seattle Seahawks defensive tackle Clinton McDonald during the second half of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Jim Harbaugh

    San Francisco 49ers head coach Jim Harbaugh reacts after talking to officials during the second half of an NFL football game against the Seattle Seahawks in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Frank Gore, Chris Clemons

    San Francisco 49ers running back Frank Gore (21) rushes past Seattle Seahawks defensive end Chris Clemons (91) during the third quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • Jim Harbaugh, Walt Anderson

    San Francisco 49ers head coach Jim Harbaugh, right, reacts as he talks with referee Walt Anderson (66) during the second half of an NFL football game against the Seattle Seahawks in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Alex Smith

    San Francisco 49ers quarterback Alex Smith (11) passes against the Seattle Seahawks during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Kyle Williams, K.J. Wright, Richard Sherman

    San Francisco 49ers wide receiver Kyle Williams (10) runs past Seattle Seahawks outside linebacker K.J. Wright (50) and cornerback Richard Sherman (25) during the second half of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Russell Wilson

    Seattle Seahawks quarterback Russell Wilson (3) passes against the San Francisco 49ers during the first quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Chris Culliver, Golden Tate

    San Francisco 49ers cornerback Chris Culliver (29) breaks up a pass intended for Seattle Seahawks wide receiver Golden Tate (81) during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Delanie Walker, Earl Thomas

    San Francisco 49ers tight end Delanie Walker (46) scores on a 12-yard touchdown reception past Seattle Seahawks free safety Earl Thomas (29) during the third quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • Braylon Edwards, Patrick Willis, Dashon Goldson

    San Francisco 49ers linebacker Patrick Willis (52) and safety Dashon Goldson break up a pass intended for Seattle Seahawks wide receiver Braylon Edwards during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • Doug Baldwin, Chris Culliver

    Seattle Seahawks wide receiver Doug Baldwin (89) catches a pass in front of San Francisco 49ers cornerback Chris Culliver (29) during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Tony Avelar)

  • Patrick Willis, Dashon Goldson, Braylon Edwards

    San Francisco 49ers linebacker Patrick Willis (52) and safety Dashon Goldson (38) break up a pass intended for Seattle Seahawks wide receiver Braylon Edwards (17) during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Marshawn Lynch, Dashon Goldson

    Seattle Seahawks running back Marshawn Lynch (24) rushes past San Francisco 49ers safety Dashon Goldson (38) during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Patrick Willis, Dashon Goldson, Braylon Edwards

    San Francisco 49ers linebacker Patrick Willis (52) and safety Dashon Goldson (38) break up a pass intended for Seattle Seahawks wide receiver Braylon Edwards (17) during the second quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Alex Smith

    San Francisco 49ers quarterback Alex Smith (11) rolls out against the Seattle Seahawks during the first quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Frank Gore, Bobby Wagner, K.J. Wright, Earl Thomas

    San Francisco 49ers running back Frank Gore (21) is tackled by Seattle Seahawks middle linebacker Bobby Wagner (54), outside linebacker K.J. Wright (50) and free safety Earl Thomas (29) during the first quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Robert Turbin, Patrick Willis

    Seattle Seahawks running back Robert Turbin (22) drops a pass in front of San Francisco 49ers linebacker Patrick Willis (52) during the first quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Marcio Jose Sanchez)

  • Michael Crabtree, Richard Sherman

    San Francisco 49ers wide receiver Michael Crabtree (15) jumps over Seattle Seahawks cornerback Richard Sherman (25) during the first quarter of an NFL football game in San Francisco, Thursday, Oct. 18, 2012. (AP Photo/Ben Margot)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head Coach Pete Carroll of the Seattle Seahawks reacts after Brandon Browner #39 intercepted a pass in the endzone against the San Francisco 49ers during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Kendall Hunter #32 of the San Francisco 49ers carries the ball for a short gain against the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head coach Jim Harbaugh of the San Francisco 49ers celebrates a win over the Seattle Seahawks on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head coach Jim Harbaugh of the San Francisco 49ers calls for a safety against the Seattle Seahawks late in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Tight end Delanie Walker #46 of the San Francisco 49ers scores a touchdown on a catch and run against free safety Earl Thomas #29 of the Seattle Seahawks in the third quarter on October 18, 2012 at Candlestick Park in San Francisco, California. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Kendall Hunter #32 of the San Francisco 49ers after gaining yards for a first down is forced out of bounds by Bobby Wagner #54 of Seattle Seahawks but the play was called back because of a penalty on the offensive line during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Field goal kicker David Akers #2 of the San Francisco 49ers celebrates a field goal against the Seattle Seahawks in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Quarterback Russell Wilson #3 of the Seattle Seahawks throws against the San Francisco 49ers in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head coach Pete Carroll talks with quarterback Russell Wilson #3 of the Seattle Seahawks after calling a time out against the San Francisco 49ers in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Running back Frank Gore #21 of the San Francisco 49ers runs for 37 yards on a play against the Seattle Seahawks at the start of the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: David Akers #2 of the San Francisco 49ers kicks a twenty eight yard field goal against the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Quarterback Alex Smith #11 of the San Francisco 49ers takes a snap against the Seattle Seahawks in the first quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: David Akers #2 of the San Francisco 49ers is congratulated by Andy Lee #4 and Will Tukuafu #48 after Akers kicked a twenty eight yard field goal against the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Linebacker Ahmad Brooks #55 of the San Francisco 49ers rushes quarterback Russell Wilson #3 of the Seattle Seahawks in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Cornerback Chris Culliver #29 of the San Francisco 49ers breaks up a pass intended for wide receiver Sidney Rice #18 of the Seattle Seahawks in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Brandon Browner #39 and Jeron Johnson #32 celebrates after Browner intercepted a pass in the endzone against the San Francisco 49ers during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Frank Gore #21 of the San Francisco 49ers after a thirty seven yard gain stumbles and is touched to the ground by K.J. Wright #50 of the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head coach Jim Harbaugh of the San Francisco 49ers looks for a holding call against the Seattle Seahawks late in the fourth quarter on October 18, 2012 at Candlestick Park in San Francisco, California. The 49ers won 13-6. (Photo by Brian Bahr/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Alex Smith #11 of the San Francisco 49ers scrambles for a two yard gain pursued by Chris Clemons #91 of the Seattle Seahawks during the first quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Evan More #82 of the Seattle Seahawks beats Chris Culliver #29 of the San Francisco 49ers on the play but More can't hold on to the pass in the second quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Frank Gore #21 of the San Francisco 49ers carries the ball for a thirty seven yard gain against the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head Coach Jim Harbaugh of the San Francisco 49ers looks on while he waits on a correct call from the officials late in the fourth quarter of an NFL football game against the Seattle Seahawks at Candlestick Park on October 18, 2012 in San Francisco, California. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head Coach Pete Carroll of the Seattle Seahawks throws a football during pre-game warm ups before their NFL football game against the San Francisco 49ers at Candlestick Park on October 18, 2012 in San Francisco, California. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Frank Gore #21 of the San Francisco 49ers carries the ball for a thirty seven yard gain breaking the tackle of earl Thomas #29 of the Seattle Seahawks during the fourth quarter of an NFL football game at Candlestick Park on October 18, 2012 in San Francisco, California. The 49ers won the game 13-6. (Photo by Thearon W. Henderson/Getty Images)

  • Seattle Seahawks v San Francisco 49ers

    SAN FRANCISCO, CA - OCTOBER 18: Head coach Pete Carroll of the Seattle Seahawks cheers on his team from the sidelines against the San Francisco 49ers in the first quarter on October 18, 2012 at Candlestick Park in San Francisco, California. (Photo by Brian Bahr/Getty Images)