The Timbers jumped out early and weathered a late Seattle fightback to claim a famous victory and a berth in the conference-deciding series.
Portland, already leading 2-1 after the first leg in Seattle, was awarded a penalty in the 27th minute when Djimi Traore handled the ball inside the box, and Timbers captain Will Johnson stepped up in front of the home fans to covert from the spot.
And just before the interval, Portland scored again. The Timbers capitalized on an Adam Moffat giveaway in midfield with a fluid passing move that ended up with Rodney Wallace feeding Diego Valeri for an inch-perfect finish into the far low corner.
Wallace was again the provider as the Timbers made it 3-0 just after the restart. A quick free kick from Will Johnson sent Wallace down the wing and his cross into the middle was headed home by Futty Danso.
DeAndre Yedlin pulled a goal back for Seattle in the 73rd minute, pouncing on a loose ball at the far post and foing well to shoot high and beat the outstretched Donovan Ricketts.
Eddie Johnson grabbed a second barely a minute later, out-leaping the Portland defense to slam home a powerful header and bring the Sounders within two in the tie and giving the visitors a glimmer of home against their archrival.
But it was false hope, and the Sounders failed to score again, coming closest when Clint Dempsey spoiled an excellent first-touch turn with a shot wide of goal in the 88th minute.
Portland will now play Real Salt Lake for the right to contest the 2013 MLS Cup final.