The visitors pressed early on as Steve Zakuani raided down the left and fired an effort at goal, which went inches past the post.
Seattle grew into the game but didn't test Donovan Ricketts until the start of the second half when Gonzalo Pineda powered a header at goal from Jalil Anibaba's cross, but the keeper tipped his effort past the post.
The Timbers responded as Zakuani drilled an effort at goal from distance which Stefan Frei couldn't hold, but the home side managed to clear the danger. At the other end, Lamar Neagle's low shot was well held by Ricketts.
Clint Dempsey came close to handing his side the lead when he latched onto a throw into the box, but Ricketts denied him with a good save, while Marco Pappa's volley on the rebound was well blocked by Jack Jewsbury.
The USA forward should have done a lot better minutes later as he tried to turned Zach Scott's header into the net from two yards out, but somehow missed the target.
However, he was to make amends as this time he did find the back of the net by diverting Pineda's shot past Ricketts after the keeper had made two brilliant saves.
Portland came within inches of finding an equaliser in the 86th minute as Gaston Fernandez drilled a shot at goal which beat the hand of Frei but clattered off the post and went wide.
The Sounders secured the win on their next attack as Pappa collected a pass from the left and curled a shot past Ricketts into the bottom corner.