"Now we're locked in," Timbers midfielder Will Johnson said. "We're in the zone."
The victory extended Portland's winning streak at Jeld-Wen Field to 16 games. The Timbers went 11-1-5 at home in the regular season with their lone loss on March 9 to Montreal. They had an MLS record 11 shutouts at home this season.
Portland pressured Seattle goalkeeper Michael Gspurning from the start. Rodney Wallace booted a shot that went just wide in the third minute, and Darlington Nagbe came close but went wide again in the 15th.
Portland broke through when Johnson converted a penalty kick in the 29th minute to go up 1-0.
Diego Valeri, who had appeared to injure his shin when he was fouled hard by Seattle defender Marc Burch, came back a few minutes later to score from a seemingly impossible angle just before the break. Valeri, who blew kisses to the crowd after his goal, was Portland's top scorer this season with 10 goals and 13 assists.
"We were hoping to get out of the first half at 0-0," Seattle coach Sigi Schmid said. "That one coming right before halftime, the goal right before halftime, the goal right after halftime, is what killed us at the end of the day. For the first 45 minutes, hats off to them, they were much better than us."
Futty Danso added a header for Portland in the 47th minute. The Sounders put up a fight, and DeAndre Yedlin's goal in the 74th minute avoided the shutout. Eddie Johnson added another three minutes later to close the gap.
The Sounders have been to the playoffs in each of the last five seasons. The Timbers, who joined MLS in 2011, are making their first trip.
"We're getting closer," Portland coach Caleb Porter said. "And this team genuinely believes we have a realistic shot at this."
The intense rivalry between the two clubs dates to 1975 when both were part of the North American Soccer league. For nearly a decade the teams have battled with the Vancouver Whitecaps for the supporter-created Cascadia Cup.
While it was sweet to defeat the Sounders, Johnson said the Timbers didn't pay much attention to the hype.
"To us, it was just another team that was in our way of getting to the next round," Johnson said.
In the opening game on Saturday in Seattle, Ryan Johnson flicked in a header early in the first half and Nagbe added a goal in the second for the Timbers. Osvaldo Alonso scored late for the Sounders, who needed to win Thursday by at least two goals to become the fourth team to accomplish the comeback since the league went to the two-leg, aggregate-goal format for its conference semifinals in 2003.
Seattle was without forward Lamar Neagle due to yellow card accumulations, but Yedlin started despite an ankle injury and forward Obafemi Martins was listed as a reserve after struggling with a groin injury.
The Timbers finished the regular season in first place in the Western Conference at 14-5-15 overall. Their 23-point improvement from last season is the biggest turnaround in MLS history.
The Sounders, who were 15-12-7, defeated the Colorado Rapids in the knockout round to advance to the semifinals.
Schmid said he was aware that some Seattle supporters were calling for a coaching change.
"I don't want to walk away. I know there's probably people out there that would like me to walk away," he said. "I think there's a good base of talent, there's a good base of people we can work with next year, but there's improvements, and there's changes we have to make."