Seattle was once sitting in a prime position for a stellar season after a 7-1-1 start, but a seven-game winless run has dropped the Sounders (7-5-4) to fourth place in the Western Conference where it sits eight points off the pace of the first-place San Jose Earthquakes.
The Timbers went two goals up inside the opening 25 minutes on Sunday as Kris Boyd and David Horst produced the telling goals.
Eddie Johnson got the Sounders to within touching distance of a comeback, but Portland (4-6-4) rode the one-goal lead to full time to improve to 16 points on the season.
Portland was dangerous from the start as Horst rattled the crossbar in the 11th minute off of a corner kick from Franck Songo'o.
It wasn't long after that the Timbers went in front, and it was the club's main scoring threat that provided the finishing touch.
Boyd bagged his fifth goal of the season when he lost his mark in the 16th minute and calmly slotted home a low cross from Steven Smith, beating Sounders 'keeper Andrew Weber with a one-time shot.
The lead was doubled nine minutes later when Portland converted from a corner kick. Horst and Songo'o connected once again, but the Timbers defender made no mistake with the header this time around as he nodded the cross into the back of the net.
Osvaldo Alonso came close to pulling one back with a stunning strike from 40 yards out just before the break, but Troy Perkins was able to get a hand to it and tip it out of play.
Seattle got on the board in the second half though, cutting the deficit in half in the 58th minute. Johnson collected a throw-in and powered into the Portland penalty area before curling a beautiful shot into the far corner, giving Perkins no chance for a save.
The match took an ugly turn at the beginning of stoppage time as both sides nearly came to blows. Fredy Montero and Lovel Palmer were shown straight red cards for their involvement in the scuffle.
It was the only sour note on an otherwise enjoyable match for the Timbers as they held on to the one-goal advantage to climb out of the Western Conference cellar.
The results also marks Seattle's first Cascadia Cup loss during the Major League Soccer era.
The Sounders went 2-0-2 against the Timbers and Vancouver Whitecaps FC in 2011, and they extended that unbeaten derby run to five games with a 2-2 draw with the 'Caps on May 19. The Timbers now lead the chase for the Cascadia Cup with four points from two matches this season.
Both sides return to the pitch on June 30 when Seattle heads to Gillette Stadium to face the New England Revolution and Portland squares off against the Colorado Rapids at Dick's Sporting Goods Park.
06/24 19:36:33 ET