It technically wasn't as lopsided as last December's 42-13 Seahawks victory here, but the 49ers sputtered all night before the largest crowd ever at CenturyLink Field (68,338).
The 49ers defense did hold strong for a 5-0 halftime deficit. That came with a price, however. Two starters were lost to injury: nose tackle Ian Williams (broken left ankle) and free safety Eric Reid (concussion).
The rivalry's physical nature took their toll and knocked out other starters: 49ers' tight end Vernon Davis (hamstring, fourth quarter) and defensive tackle Ray McDonald (right ankle, fourth quarter) and Seahawks left tackle Russell Okung (foot, first quarter).
The 49ers committed 12 penalties for 121 yards.
Anquan Boldin, who had 13 catches for 208 yards in last week's opener, was held without a reception until 9:20 remaining, when he caught a 7-yard pass.
The Seahawks' dominance with their defensive line was reflected by the 49ers' running stats: Kaepernick often had to scramble and finished with nine carries for 87 yards. In comparison, Frank Gore was limited to 16 yards on his nine carries.
The Seahawks' lead grew to 19-3 with 13:44 remaining, when Russell Wilson beat the 49ers' blitz and found a wide open Marshawn Lynch with a 7-yard touchdown pass. Aiding and abetting that drive were two big penalties on the 49ers: Nnamdi Asomugha's 40-yard pass interference call and Aldon Smith's 15-yard unsportsmanlike conduct for slapping the helmet of a Seahawks lineman.
The 49ers offense failed to capitalize with touchdowns on two drives inside the 10-yard line. On the first, Kaepernick had a third-down pass intercepted at the 1 by Earl Thomas on the 49ers' second series. In the third quarter, Kaepernick got stopped for no gain on a third-and-goal scramble from the 3, setting up Phil Dawson's 21-yard field goal for a 12-3 deficit.
The 49ers had only 62 yards (and four first downs) before marching 72 yards for that Dawson field goal.
Kaepernick's second turnover of the night (a strip-sack fumble) led to Seattle's second scoring drive, ending with Steven Houschka's 30-yard field goal for a 5-0 lead 5:52 before halftime. Kaepernick got stripped by Cliff Avril on third-and-10, and the Seahawks' K.J. Wight recovered at the 49ers' 29-yard line.
That offensive miscue came on the heels of an outstanding effort by the 49ers defense, which stopped Wilson on a fourth-and-1 sneak.
The Seahawks took a 2-0 lead when 49ers fullback Bruce Miller got called for holding in the end zone. On second-and-12 from the 4-yard line, Miller tackled linebacker Malcolm Smith to the ground as Kaepernick escaped pressure and attempted a pass to Frank Gore.
One drive into the second half and the game's first touchdown was born, via Marshawn Lynch's 14-yard run up the middle. That gave the Seahawks a 12-0 lead, and that drive was keyed by a 51-yard catch by Doug Baldwin at the 49ers' 20.