Portland's Julio Cascante deflected the ball into his own net in the 76th minute and the Seattle Sounders won their franchise-record seventh consecutive game on Sunday night.
The Sounders also moved past the Timbers in the race for the Western Conference's playoff spots for the first time this season.
Goalkeeper Stefan Frei made three saves for his sixth clean sheet of the season for the Sounders, who stretched their unbeaten streak to 10 matches. The Timbers suffered their fourth straight defeat after a 15-match unbeaten run.
The own goal came after Sounders defender Kim Kee-hee made a run down the right wing. His cross for Raul Ruidiaz glanced off Cascante's leg and trickled into the far left corner of the net, leaving goalkeeper Jeff Attinella with no chance.
The Timbers dominated the offensive chances in a scoreless first half, outshooting the Sounders 14-2.
The Timbers had three good chances just inside the 10-minute mark. Diego Valeri put a 30-yard free kick just wide of the left post in the eighth minute.
Sebastian Blanco also had a chance in the eighth after a Seattle turnover deep in its own end, but Osvaldo Alonso knocked the ball away at the top of the six-yard box before Blanco could get off a shot.
Less than a minute later, Cascante headed a corner kick from Valeri just over the crossbar.
Valeri also had a good chance early in the second half, but Frei dove to the left post to knock away the 25-yard shot.
The Sounders started getting some better chances midway through the second half after Will Bruin, who is tied for the team lead with six goals, came on as a substitute.
That opened up space for Ruidiaz, who couldn't quite catch up to one through ball that Attinella charged and smothered. Ruidiaz also had a bicycle kick from the middle of the penalty area go wide left in the 89th minute.