The Timbers brought a 2-1 advantage from the first leg in Seattle into Thursday's match, and the home side decided to take the game to the Sounders from the start with Will Johnson converting a penalty kick after 29 minutes before Diego Valeri doubled the lead shortly before halftime.
Mamadou Danso made it 3-0 to the Timbers in the 47th before Seattle mounted a brief comeback with goals from DeAndre Yedlin and Eddie Johnson two minutes apart to make it 3-2 to Portland with 15 minutes to play.
But the Timbers were able to stem the tide and hold on for the 5-3 aggregate win, sending Caleb Porter's men to Real Salt Lake on Sunday for the first leg of the Western Conference final.
Despite bringing a one-goal lead into Thursday's match Portland didn't sit back and Rodney Wallace squandered a great chance for the hosts in the opening two minutes.
The Timbers seized the lead in the 29th when Jack Jewsbury attempted to chip the ball past Seattle defender Djimi Traore inside the penalty area, only for Traore to handle the ball.
Will Johnson stepped to the penalty spot and sent goalkeeper Michael Gspurning the wrong way, giving the Timbers a 3-1 aggregate lead that would only grow larger.
Valeri scored in the 44th after taking a pass from Wallace and finishing off the play in traffic with some nice footwork, making it 2-0 to Portland on the night at halftime.
Things only got worse in the 47th as a quick free kick allowed Wallace to cross the ball from the left wing to the near post, where Danso turned home a header from six yards.
Seattle showed a bit of life in the 74th when Yedlin scored from close range after a flicked header, and things got a little more interesting when Eddie Johnson headed home Yedlin's right-wing cross two minutes later.
Clint Dempsey could have made things interesting in the 88th minute for Seattle, but he shot just wide of the post from 10 yards and Portland saw out the rest of the match to advance.
11/08 01:17:53 ET