The delay came in the first quarter with the game scoreless.
Seattle (2-0) dominated upon the resumption, using three second-half touchdowns by Marshawn Lynch to win going away.
It was the 49ers' second blowout loss in Seattle, having fallen 42-13 last December. San Francisco (1-1) plays host to Seattle on Dec. 8 at Candlestick Park.
Seattle went on identical 10-play, 80-yard drives the first two times it had the ball in the second half to take control.
Lynch scored on a 14-yard run to cap the initial mark, then on a seven-yard pass from Russell Wilson to cap the second drive.
The scoring pass was part of a second-half turnaround for Seattle's second-year quarterback, who was just 2-for-10 in the first half.
Wilson went 4-for-5 for 80 yards in the third quarter as the Seahawks finally took the upper hand, and he finished 8-for-19 for 142 yards, one touchdown and one interception.
Lynch gained 98 yards on 28 carries as Seattle outgained the 49ers 290-207.
With a record CenturyLink Field crowd of 68,338 going crazy throughout, despite the delay, the 49ers offense could never get on track. Quarterback Colin Kaepernick completed 13 of 28 passes for 127 yards with three interceptions. He also ran nine times for 87 yards.
The Seahawks led 5-0 at the end of a strange first half that featured an hour-long delay due to lightning.
The delay came with 3:13 left in the first quarter.
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