Lynch had been listed as questionable, and coach Pete Carroll had said on Friday he expected Lynch to play. Lynch had played last week after being listed as questionable in the days leading up to the game.
However, this time Lynch was on the inactive list before the game.
Also among the inactive for the Seahawks were wide receiver Paul Richardson and linebacker Bruce Irvin, both of whom were injured in last week's game against the Cardinals.
Running back Carlos Hyde was among those inactive for the 49ers because of foot injury.