On the play, Valencia got control of a long ball from Will Johnson, beat a defender and put it past Vancouver goalkeeper Brad Knighton to erase a 2-1 deficit.
The Whitecaps protested the goal, saying the ball touched Valencia's arm before the score.
Johnson also found the net for the Timbers (5-1-6), who strengthened their hold on second place in the Western Conference while extending their unbeaten streak to 10 games.
Camilo Da Silva Sanvezzo and Gershon Koffie each scored for Vancouver (3-5-3).
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