Lynch ran the ball 28 times for 98 yards, including touchdowns of 14 and 7 yards, and added three receptions for 37 yards and a score as the Seahawks (2-0) ran their regular-season home unbeaten streak to nine games.
Seattle picked off 49ers quarterback Colin Kaepernick three times and recovered two fumbles on its way to the convincing win over its division rival.
Russell Wilson completed 8-of-19 passes for 142 yards, a touchdown and an interception while also picking up 33 rushing yards on 10 carries.
Kaepernick managed only 127 yards on 13-of-28 passing, adding 87 yards on the ground with a lost fumble on nine carries for San Francisco (1-1).
The start of the game was delayed by an hour due to lightning in the vicinity of sold-out CenturyLink Field.