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Walker ran over the middle, took the pass from Smith and scampered just inside to the left pylon for a touchdown in the third quarter. What a fitting turnaround for the tight end, who broke his jaw in two places in a Week 16 win at Seattle last season when he took a knee to the face from linebacker Leroy Hill and didn't return until the NFC championship game.
Steven Hauschka kicked field goals of 52 and 35 yards to give Seattle a 6-3 lead. He also missed wide left from 51.
On a relatively warm and windless night at Candlestick Park, two of the NFL's top defenses dominated.
NaVorro Bowman clobbered Russell Wilson as he threw and Dashon Goldson intercepted the overthrown pass at the San Francisco 27. Wilson walked slowly to the sideline after absorbing the punishing hit from the All-Pro linebacker.
The three-way tie atop the NFC West - with San Francisco, Seattle and Arizona all with 4-2 records - was set to be broken. The St. Louis Rams are 3-3.
Defense has been perhaps the biggest turnaround for a division some called the NFC Worst a couple of years ago. Seattle (15.3) and San Francisco (15.7) rank second and third, respectively, in points allowed per game.
Thursday night was no different.
Smith and San Francisco struggled to move the ball for the second straight week, settling for a 38-yard field goal by David Akers in its best drive of the opening half. Until Walker's score with 4:29 left in the third quarter, San Francisco had not scored in six quarters.
Wilson led a 10-play, 62-yard drive that started from its own 4-yard line before San Francisco shut down Seattle and Hauschka kicked his first field goal. Wilson completed 6 of 16 passes for 103 yards through three quarters as Seattle scored first for the seventh straight game to start the season.
Michael Crabtree caught a 16-yard pass from Smith on San Francisco's second drive, placing his hand on the ground to avoid going down and making three defenders miss along the sideline. The completion moved the 49ers to the Seattle 19 before the All-Pro Akers kicked the tying field goal late in the first quarter.
Goldson got a 15-yard unsportsmanlike conduct penalty for jawing with Marshawn Lynch during Seattle's first scoring drive. Lynch, who ran for 107 yards in the last meeting as San Francisco's streak of not allowing a 100-yard rusher ended at 36 games, had 88 yards on 15 carries.
San Francisco still missed opportunities.
Ted Ginn Jr. returned a punt 38 yards to midfield with 1:27 remaining before halftime. Smith threw the ball away twice under pressure before Bruce Irvin sacked him on third down to force a punt.
Malcolm Smith left with a concussion after making a hard, helmet-first tackle on Ginn during the opening kickoff. Seattle's backup linebacker was helped off the field by trainers and the team said he would not return.
San Francisco was looking to rebound from an embarrassing 26-3 defeat at home last week to the Super Bowl champion New York Giants, the most lopsided loss under coach Jim Harbaugh. The 49ers are 4-0 after a loss in Harbaugh's tenure.
They also swept the season series against Seattle last year for the first time since 2006.
The brewing rivalry between the last two division champions only heated up when Harbaugh and Seattle's Pete Carroll were reunited on opposite sidelines last year. Harbaugh has won the last three against Carroll.
That streak goes back to Harbaugh's win at Stanford against Carroll's Southern California team in 2009, when the Cardinal routed the Trojans 55-21. Harbaugh even had his team attempt a late 2-point conversion with the game out of reach that prompted Carroll's infamous midfield confrontation afterward, asking Harbaugh, "What's your deal?"