In an impressive exhibition of counter-attacking football, the Timbers soaked up pressure in Seattle throughout the first leg of their Western Conference semi-final against the Sounders and decisively cut through the home side's defence on two occasions.
Ryan Johnson struck on 14 minutes for the Conference champions, while Darlington Nagbe scored after half-time for Portland.
But Seattle ensured the Timbers will only take a one-goal aggregate lead back home ahead of Thursday's second leg after Osvaldo Alonso scored in the 90th minute.
Seattle had the majority of possession at CenturyLink Field on Saturday, making 438 passes compared to the their Cascadia Cup rivals' 303, but the home side had to settle for opportunities from set pieces early in the match as Portland's defence held firm.
In the 15th minute, the Timbers opened the scoring thanks to a rapid counter-attack with Diego Chara switching play to right-back Jack Jewsbury, who picked out Johnson at the near post and the Jamaican striker glanced a header past Seattle goalkeeper Marcus Hahnemann.
Clint Dempsey was the Sounders' best player and almost scored twice in the opening half hour from direct free-kicks with Portland goalkeeper Donovan Ricketts spectacularly denying the United States international in the 20th minute.
Ricketts was beaten 10 minutes later but Dempsey's effort only clipped the top of the crossbar.
While Seattle continued to have more of the ball, the visiting back four of Michael Harrington, Po Modou Kah, Mamadou Danso and Jewsbury remained strong and 20 minutes after the break, Nagbe made it 2-0.
Substitute Khalif Alhassan drove inside from the right and picked out Nagbe's diagonal run, setting up the 23-year-old winger to smash his strike past Hahnemann.
The Sounders continued to push but Johnson could have made it 3-0 for Portland on the break with seven minutes left only for his shot to be deflected wide before Dempsey hit the bar with an 87th-minute header.
But in the final minute of regulation time, a long throw was flicked on to Alonso and the 27-year-old midfielder smashed his volley home from the penalty spot.
In the Eastern Conference semi-finals, New England Revolution defeated visiting Sporting Kansas City 2-1.
Sporting had the best chances of the first half with Teal Bunbury and Aurelien Collin both having efforts deflected wide of the goal by defenders in the space of two minutes.
But 10 minutes after half-time, New England took the lead when Andy Dorman finished from less than a metre out after Jimmy Nielsen failed to hold onto Diego Fagundez's strike.
The Revolution doubled their lead in the 67th minute when Lee Nguyen found Kelyn Rowe in the driving rain and the 21-year-old midfielder slotted his shot into the corner of the net, although Kansas City struck back almost immediately with Collin converting after New England failed to clear their defensive penalty area.
