Following a rather tame first 45 minutes Portland got things going in the 51st minute as Alvas Powell scored his first MLS goal.
Maximiliano Urruti followed with a second tally 15 minutes from time, and Rodney Wallace capped the scoring four minutes later to give the Timbers their second win in four games.
Vancouver continues to struggle finding wins and the club has now won just once in its last nine outings.
Diego Valeri went close in the 37th minute for Portland with a shot that just missed the upper left corner of the net, but it was as close as either side came to opening the scoring in the first half.
Valeri then set up the first goal as he found space on the wing to drive a cross into the penalty area that was turned home at the near post by the head of Powell.
Darren Mattocks came off the bench for the Whitecaps and got in on goal but was denied in a one-on-one situation by goalkeeper Donovan Ricketts.
Nine minutes later, Portland doubled its lead when Michael Harrington did some good work to create space and pull the ball back for Urruti, who was left open to slot the ball high into the net.
Darlington Nagbe set up the third goal for Wallace four minutes later and there was no way back for Vancouver.