Chilean midfielder Pedro Morales was the hero with two first-half penalties as the Whitecaps recorded their first-ever win against the Timbers, though it could have ended a lot differently in Portland.
Portland had closed to within a goal thanks to strikes from Gaston Fernandez and Will Johnson inside the final 14 minutes but the Whitecaps held on to end their nine-game winless run against the Timbers.
The Whitecaps, who are unbeaten in six league games, leapfrogged Dallas into fourth position, having collected 20 points from 12 matches thus far.
As for the Timbers, they remain eighth in the West after suffering their first defeat in six games.
Portland made a dream start on home soil thanks to Argentinean striker Maximiliano Urruti, who opened the scoring in the third minute - his sixth goal of the season.
But it was one-way traffic from that point as the Whitecaps netted three unanswered goals before half-time.
Former Malaga midfielder Morales converted a 16th-minute penalty and he stepped up to the spot again 10 minutes later to put the visitors ahead.
Erik Hurtado doubled Vancouver's advantage three minutes into added time before Jordan Harvey seemingly put the result beyond doubt four minutes into the second half.
Portland were given a glimmer of hope in the 77th minute, when Fernandez found a way past Danish goalkeeper David Ousted.
The Timbers set up a nervy finish after Johnson scored four minutes from time and they came close to levelling proceedings but Rauwshan McKenzie's header flashed past the post as Vancouver secured maximum points.
Elsewhere on Sunday, Colorado Rapids climbed up to third in the West after accounting for Houston Dynamo 3-0.
A first-half brace from Jamaica international striker Deshorn Brown and Kamani Hill's 51st-minute goal set up the Rapids for a comprehensive win at Dick's Sporting Goods Park.
The Rapids, who have won back-to-back games, are eight points adrift of Conference leaders the Seattle Sounders.
Though, the Colorado-based team have played a game less than the Sounders.
Meanwhile, fourth-placed Houston missed the chance to go third in the Eastern Conference.
In Sunday's early game, Landon Donovan was on target again as the Los Angeles Galaxy played out a 1-1 draw at Chicago Fire.
Jeff Larentowicz scored a 68th-minute penalty but Donovan equalised six minutes later to ensure honours were even at Toyota Park.
Donovan, who was controversially overlooked for the United States' FIFA World Cup squad, has now scored three goals in two games.
