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Tony Avelar, Associated Press
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.

SAN FRANCISCO — Pete Carroll pulled up a chair and sat next to Russell Wilson in one corner of Candlestick Park's visiting locker room, listening to his rookie quarterback and asking questions.

Both are still searching for some answers.

Wilson threw for 122 yards and an interception, his receivers dropped several passes and the Seattle Seahawks lost 13-6 to the San Francisco 49ers on Thursday night to fall out of a first-place tie in the NFC West.

Seattle (4-3) has lost all three division games, and all three came on the road.

"The way we lost was frustrating," said Wilson, who completed 9 of 23 passes. "We could have done some things better. I could have done some things better."

Now Seattle — and everyone else — is back to chasing San Francisco atop the division.

Smith threw a 12-yard touchdown pass to tight end Delanie Walker late in the third quarter for a 10-6 lead. San Francisco (5-2) relied on its dominant defense to harass Wilson and hold off Seattle's final rally.

"We found ourselves in a real slugfest here today," Carroll said. "I'm not surprised it could have gone that way with two good defenses and two teams committed to running the ball. And there was plays in this game that I'll always want to know, what would have happened if we made this play or made that play? It was so close."

Frank Gore ran for 131 yards and the 49ers made just enough plays to win a defense-dominated game that featured two teams allowing fewer than 16 points per game. Arizona (4-2), which plays at Minnesota on Sunday, still has a chance to keep pace with San Francisco this week.

Already 0-3 in the division, Seattle is in a hole before even hosting a league foe.

Walker's score was San Francisco's first touchdown in seven quarters after an embarrassing 26-3 defeat against the defending Super Bowl champion New York Giants on Sunday, the most lopsided loss in coach Jim Harbaugh's tenure. The tight end broke his jaw in two places at Seattle last Dec. 24 and sat out until the NFC title game.

Smith went 14 of 23 for 140 yards and an interception in another subpar performance. San Francisco's defense hung tough down the stretch, holding NFC rushing leader Marshawn Lynch to 103 yards.

Now it's now Harbaugh 3, Carroll 0 since these coaching rivals started facing off in the NFL last year after all those memorable moments at Stanford and Southern California.

"Both teams played like crazy and beat the heck out of one another," Carroll said. "That's kind of what this division has become. It's turned. It's a division that you can count on hard defense and running the football. I don't mind that one bit."

But losing to Harbaugh will sure bug Carroll again.

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

"We had a long drive in the third quarter. We just kind of felt them start to give up a little bit, and they knew we were just going to keep running the ball on them," 49ers right guard Alex Boone said. "It was more of, 'Let's get back to our roots and do what we're good at,' that's being physical, pounding the ball. Frank's a great runner."

After Walker's touchdown, Dashon Goldson intercepted a deep pass by Wilson to thwart Seattle's next drive after NaVorro Bowman clobbered the former Wisconsin 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.

Wilson, who spoke leading up to the game that he couldn't wait for his introduction to this heated rivalry, was sacked twice and never looked in rhythm. 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.

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.

"We've got to figure something out," said wide receiver Golden Tate, who had two drops. "We've got to figure out a way to get it done. It's not over. The season's not over."

NOTES: Seattle lost LB Malcolm Smith to a concussion on the opening kickoff, then WR Doug Baldwin later injured his ankle and did not return. ... 49ers WR Mario Manningham was inactive with a shoulder injury. ... Ted Ginn Jr. had a 38-yard return late in the first half for the 49ers.

Antonio Gonzalez can be reached at: www.twitter.com/agonzalezAP