The Seahawks built a 13-0 halftime lead in the exhibition contest on two field goals from Steve Hauschka and a 2-yard run by Vai Taua.
Flynn, who completed 11-of-13 passes for 102 yards, hit Cooper Helfet with a 4-yard scoring throw in the third.
Oakland did not reach 100 yards for the game until the final minute, made just five first downs and settled for a field goal with 15 seconds remaining to avoid the shutout.
Seattle will begin its regular season at Arizona and Oakland will host San Diego.
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