A barnstorming opening took the home team into an early lead, and it held on to take all three points.
Kekuta Manneh scored the opener in the 10th minute. Running into the box with the ball at his feet, his first shot rebounded off the bar, but his follow-up effort was dinked over Jon Busch and found the back of the net to make it 1-0.
It didn't take long for the Whitecaps to make it 2-0. Darren Mattocks was brought down by Victor Bernardez inside the box, and Pedro Morales stepped up and tucked him the spot kick.
Barely a minute later, Morales smashed one in from distance and gave the Whitecaps a commanding lead. With the 'Quakes defense standing off, the Chilean blasted a shot from outside the area to send his side 3-0 up.
San Jose pulled one back shortly before halftime. Jay DeMerit was judged to have unfairly shoved Alan Gordon to get to a ball into the box and Chris Wondolowski did the honors from the spot.
Wondolowski grabbed another in second-half stoppage time. A weak clearance from DeMerit fell to the San Jose star, who turned and fired a shot past David Ousted to make it 3-2
Vancouver's win takes the 'Caps to 3-2-4 on the season. San Jose falls to a troubling 1-3-3 on the year.