The visitors could have taken the lead early on when Jack Jewsbury rose highest in the penalty area to head Diego Valeri's corner at goal but DeAndre Yedlin was on hand to head the ball off the line.
Ryan Johnson should have put Portland ahead minutes later, when Valeri threaded a through-ball to leave him one-on-one with Michael Gspurning but the keeper made himself big for the save.
Valeri himself became the next Timbers player to somehow not find the net as his curling effort from the edge of the box beat Gspurning but clattered off the post and bounced clear.
After the break, Seattle took the lead when Eddie Johnson coasted into the penalty area unmarked to head Mauro Rosales's free kick past Donovan Ricketts into the net.
Eddie Johnson and Clint Dempsey had opportunities to double the home side's lead but they were kept at bay by good stops from Ricketts and Valeri, who headed the former Tottenham Hotspur man's effort off the line.
Late in the game Darlington Nagbe almost found an equaliser for Portland but his powerful effort was tipped over by Gspurning, which sealed the win for the Sounders.