Clint Dempsey and Marco Pappa struck in the second half at CenturyLink Field as the Sounders bounced back from their surprise loss to the Vancouver Whitecaps in their last league outing.
Seattle's win was their second in five days over the Timbers, having eliminated Portland in the US Open Cup quarter-finals on Thursday.
Sigi Schmid's men climbed well clear atop the Western Conference, while the Timbers are struggling in eighth.
Both teams struggled to create opportunities in the first half as Portland winger Steve Zakuani troubled his former side.
The Sounders almost took the lead in the 47th minute.
Gonzalo Pineda's header was bound for the bottom corner, only for Donovan Ricketts to produce a fine diving save.
Zakuani tested Stefan Frei from range soon after and Dempsey missed an open goal just before the hour-mark.
United States international Dempsey would make no mistake in the 71st minute.
Ricketts made a superb double save after a scramble in the area and Pineda fired an effort which was heading wide before Dempsey turned it in.
The Timbers were unlucky not to be level in the 86th minute as Gaston Fernandez's 30-yard effort hit the outside of the post.
Pappa sealed the win just moments later, collecting a Lamar Neagle pass before tucking away a finish from the centre of the area.
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