After Wondolowski's fifth goal of the year provided the equalizer in the 68th minute, the Quakes grabbed the lead 4 minutes later.
After bringing the ball down the left side, Ramiro Corrales sent a long cross into the box, where Gordon put his forehead on it with a diving header that sent the ball to the far back post.
Wondolowski added an insurance tally only 4 minutes later and San Jose (4-1-0) returned home with a win following a 2-0 road trip.
The Whitecaps (2-1-2) sustained their first defeat of the season, managing only a single goal from Sebastien Le Toux.
Notable deaths of 2014 [PHOTOS]