Jimmy Garoppolo completed only three of seven passes on the opening possession, and Matt Breida and Tevin Coleman combined for only 4 yards on four carries.
Yet, the 49ers have a 3-0 lead after one possession.
New kicker Chase McLaughlin, filling in for the injured Robbie Gould, was good on a 43-yard field goal with 8:19 remaining in the first quarter.
The 49ers benefited from two defensive penalties on the Seahawks on third down as well as an offsides penalty on Jarran Reed.
Officials flagged Jamar Taylor for defensive holding on a third-and-five pass by Garoppolo that negated an interception by Shaquill Griffin, who returned it 7 yards to the San Francisco 46.
Three plays later, on third-and-six, Garoppolo completed a 5-yard pass to Emmanuel Sanders. But Tre Flowers was cited for pass inference, giving the 49ers a first down.
The Seahawks had 15 yards in penalties on the drive. The 49ers had 30 yards.
Defensive end Jadeveon Clowney went out on the first series. Clowney is probable to return with a shoulder injury.
The Seahawks went three-and-out on their first series with D.J. Jones getting a sack of Russell Wilson on third down.