The Seahawks made a bright start against their NFC West rivals as Russell Wilson fired the ball through the middle to Tyler Lockett for a 24-yard touchdown.
Seattle extended their lead further before the end of the first quarter as Thomas Rawls, who started in place of the injured Marshawn Lynch, scrambled across from two yards out.
The visiting side struggled to get their offense going in the first quarter though, punting three times after picking up just two first downs in the opening 15 minutes.
Seattle continued to see the majority of the ball in the second quarter, with Rawls making another big run to set up Lockett for his second touchdown of the game.
The 49ers did manage to get off the mark in the final seconds before half time though, with Quinton Patton converting a first down before Blaine Gabbert fired the ball into the endzone for Vance McDonald, ensuring that San Francisco were not shut out in the first half.