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Something had to give on Thursday night at Candlestick Park.

Entering the NFC West showdown between two first-place teams, the 49ers toted the NFL’s best rushing attack, while Seattle boasted the league’s No. 2 rush defense. When the dust settled after the 13-6 San Francisco win, it was clear who won the battle between the teams’ strengths.

And it wasn’t even close.

Frank Gore showed why he’s the franchise’s all-time rushing leader, slicing the Seahawks defense for a season-high 131 yards on 16 carries, while also gaining a game-high 51 yards on five catches.

“I just got in a rhythm and my o-line and receivers did a great job blocking,” Gore said. “I feel like once I get in rhythm, I feel like I can’t be stopped.”

At times, Gore certainly looked unstoppable under the Thursday night lights. That’s because the offensive line opened gaping holes for him all night, shoving aside a defense that had given up an average of just 70 yards per game.

By the time Alex Smith took a final knee to run out the clock, the 49ers had piled up 175 yards on 32 carries, right on par with the team’s 176.8 yard average per game.

“When everybody is on one page, we can do great things in the running game,” Gore said.

As much as Gore appreciated his linemen creating big running lanes, they appreciated his ability to finish runs with power.

“Frank made some unbelievable runs,” center Jonathan Goodwin said.

Following the game, fired-up 49ers Coach Jim Harbaugh told reporters the second half featured the most physical 30 minutes of football he had ever seen from his team.

That statement was directed at both sides of the ball. Not only was the defense meeting Seattle’s punishing running back Marshawn Lynch at the point of attack, but the linemen were mauling at the line of scrimmage.

“It was more, ‘Let’s get back to our roots and let’s do what we’re good at,’” guard Alex Boone said. “And that’s being physical, pounding the ball. Frank’s a great runner. I mean the guy can hit a slice.”

Gore really got going after intermission, as he picked up 92 of his yards on 10 second-half carries. Boone said he felt like the 49ers really wore the Seahawks down in the third quarter, especially on the 10-play, 86-yard drive that ended with a 12-yard touchdown catch by Delanie Walker to put San Francisco up 10-6.

“This Thursday night game just came down to who wanted to be a tougher guy,” Boone said. “It (stinks) playing on Thursday, you’re tired from the Sunday game, but the battle of wills is going to happen and you’ve got to bring your ‘A’ game and just got to say, ‘I’m going to be tougher today.’”

Gore was a one-man wrecking crew on the touchdown drive, as he accounted for 50 yards from scrimmage on series. In all, the 49ers offensive co-captain produced his team’s three longest plays on the night, including fourth-quarter runs of 37 and 20 yards. He now has 32, 100-yard games in his career, the most of any back since 2005.

“We knew coming in that we had to be successful in the run game to win this game,” said Pro Bowl tackle Joe Staley, who returned to action after suffering a concussion last wek. “It’s a tall task. They were (No. 2) coming into this game against the run, but we were up to the challenge. Frank was hitting the holes hard, Kendall (Hunter) was hitting the holes hard. I’m really proud of the whole offense, the way they stuck with it.”

True to form, the 49ers coaching staff attributed the second-half success to the players on the field for executing and making plays. Vice-versa, the players showered Harbaugh and offensive coordinator Greg Roman with praise after putting the offense in position to win.

Gore had especially lofty words for Roman, who has won over the entire 49ers huddle with his innovative play-calling and clearly made some smart halftime adjustments on Thursday.

“Playing with G-Ro for my second year, I think he’s probably the best coordinator I’ve ever played with especially in the running game,” Gore said. “He’s a genius. We’ve just got to keep it up, as a team, as a unit.”

On the other side of the ball, the 49ers were able to weather the storm from Seahawks running back Marshawn Lynch. Though the Oakland native had 19 carries for 103 yards, he was shut out of the end zone and for the most part contained all night.

The 49ers expected a physical battle from Lynch and company and they got it. Justin Smith labeled Lynch the toughest running back he’s faced since Baltimore’s Jamal Lewis, commending the bruising runner for lowering his shoulder at the point of contact.

Meanwhile, Seattle wunderkind Russell Wilson fell back to earth against the San Francisco defense, going 9 of 23 for 122 yards and an interception.

“Coming off a loss, we wanted to go out there and get that mojo back,” Patrick Willis said. “We never lost it, but at the same time, you never want to lose a game. It’s a bad taste in everyone’s mouth, we just knew we had to come out and play great football against this team tonight.

Pass Defense Corrals Wilson

San Francisco’s secondary kept up its domination of opposing quarterbacks again on Thursday. The unit entered as the No. 2 pass defense in the NFL and improved to the league’s top-ranked group for the time being.

After holding Wilson to a season-low 122 yards and a 39.1 completion percentage (9 of 23), the 49ers are giving up an average of just 173.4 passing yards per game.

“We have a bunch of guys back there that – we’re not going to back down,” Donte Whitner said.

Dashon Goldson provided the game’s only turnover of the game in the third quarter. The Pro Bowl 49ers safety tracked down a long pass from Wilson after NaVorro Bowman applied serious pressure, before hauling it in near the 49ers sideline at the San Francisco 27-yard line. It marked Goldson’s second interception of 2012 and his eighth since the start of the 2011 season.

“I just read the quarterback pretty good,” Goldson said. “Our front seven did a good job of rushing the quarterback, he put some air under the ball and I just ran underneath it.”

Special Teams Shows Up

Ted Ginn Jr. didn’t quite have the same impact on the game like he did in last year’s home contest against the Seahawks, when he had punt and kickoff returns for touchdowns to seal the win, but he was effective nonetheless.

Ginn was especially deadly returning punts, as he broke off a 38-yarder in the second quarter to give the 49ers the ball at the 50-yard line, while also pulling off a big 16-yard return in the fourth quarter. Ginn also reclaimed kickoff return duties from Kyle Williams on Thursday night and showed why he’s still one of the game’s best return men, rattling off a 26-yard return to start the game.

Aside from Ginn, Harbaugh said he was also pleased with the team’s coverage units and the specialists. Akers nailed a 38-yard field goal to extend his franchise record to 23 straight games with a conversion, while Andy Lee routinely pinned the Seahawks within their 10-yard line on his five punts for the evening.

“Dynamite,” Harbaugh said. “Coverage was great. Against a tremendous returner (Leon Washington) and Seattle had been very good on special teams. And it was lights out on the coverage teams. And then Ted Ginn again had a great game tonight. We just played really well on special teams.”

Haggans Makes 49ers Debut

Linebacker Clark Haggans made his 49ers debut on Thursday night, occasionally filling in for Aldon Smith, who recorded a sack to bring his 2012 total to 5.5 on the night. Haggans, a 13-year vet signed from Arizona this offseason, did not record an official tackle on Thursday, but he laid a big hit on Willis while trying to tackle Lynch in the second half.

“He was about to knock me out,” Willis said with a laugh. “I said, ‘Man, that’s the biggest hit on me all year and it was by my own man.’”

Hard-hitting jokes aside, Haggans said he was happy to contribute to a 49ers win with his teammates. With the victory, San Francisco (5-2) is in sole possession of first place in the NFC West.

“It was like being at home,” Haggans said. “It was good to get back out there and run around and get some live action. We’ve just got to keep it going. This feeling is definitely better than it was five days ago.”