Steven Hauschka kicked his third goal of the game for Seattle and Phil Dawson put San Francisco on the board with a 40-yard field goal, and the Seahawks led the 49ers 16-3 after the third quarter Thursday night.
Seattle cost itself key chances to build the lead because of penalties, including an offensive pass interference against Robert Turbin that nullified Paul Richardson's 7-yard touchdown catch from Russell Wilson.
Hauschka also kicked two second-quarter field goals as Seattle held the 49ers scoreless at home in the first half for the first time since Tampa Bay did so on Nov. 21, 2010.
Richard Sherman intercepted Colin Kaepernick's deep third-down pass on the right sideline in the first quarter to help set up Wilson's 13-yard touchdown pass to Turbin.
A wide-open Turbin easily took the ball down the left sideline on a pretty catch-and-run before beating cornerback Chris Culliver into the end zone to give the defending Super Bowl champions the early edge in the first of two meetings between the NFC West rivals in a three-week span.
Sherman — who at one point blew kisses with both hands to the crowd — nearly had another pick late in the first half, when Seattle outgained San Francisco 202-71. The 49ers were held to 23 yards rushing and shut out in the first half for the first time this season.
Both teams came in at 7-4 and trying to stay in the playoff chase, facing off 10 months after a heated NFC championship game last January that Seattle won by six points on the way to the Super Bowl title.
Wilson scrambled every which way to burn a pair of 49ers rookies on Seattle's next scoring drive.
Dontae Johnson missed Wilson twice then Chris Borland was left diving for the quarterback's ankles as he lofted a short pass to Tony Moeaki for a 63-yard gain. He was stopped at the 1 by Perrish Cox and Chris Culliver.
But Marshawn Lynch was stopped for no gain, Wilson took a sack and threw incomplete as Seattle settled for Hauschka's 21-yard field goal. He later added a 36-yarder.
Former 49ers player Ricardo Lockette stripped punt returner Cox to force a fumble recovered by Seattle to give the Seahawks one more chance, but they failed to capitalize.
The 49ers have won five straight home games in the rivalry, but this marked Seattle's first trip to new $1.3 billion Levi's Stadium.
San Francisco's Michael Crabtree went down 56 seconds into the game after landing awkwardly on his left side following a 5-yard reception, Kaepernick's first throw of the game and on the second play from scrimmage. Safety Kam Chancellor tackled him from the side, then checked on the wideout as he walked off on his own. The 49ers said Crabtree had a rib injury, but he later returned.
Crabtree was at the center of the decisive play in January's NFC championship game, when Sherman deflected a pass headed his way in the end zone and Malcolm Smith intercepted it with less than a minute remaining in the Seahawks' 23-17 victory.
Seattle went three-and-out on its first two series, hurt the initial drive by a clipping penalty. 49ers defensive tackle Ray McDonald injured a finger on the play and was replaced by Tony Jerod-Eddie.
Kaepernick was just 3 for 7 with the interception and a sack for a 10.7 passer rating in the opening quarter, while Wilson completed 5 of his first 7 passes for 47 yards and a 129.2 rating.
In a lighthearted moment before kickoff, 49ers coach Jim Harbaugh's black hat blew off during the national anthem and landed on the lowest white stripe of a flag that covered the entire field. A San Francisco staffer quickly retrieved the cap just in time as the flag was being rolled up after "The Star-Spangled Banner."
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