Wondolowski was seeking his eighth goal of the season with the shot from inside the penalty box in the 91st minute, but he couldn't it get past the Whitecaps defenders, and the Earthquakes (10-11-8) saw their six-game home winning streak snapped.
Substitute Darren Mattocks had the best scoring chance for Vancouver (10-10-8), which saw the return of captain Jay DeMerit, who went down with a ruptured Achilles tendon in the season's first game.
The Whitecaps have managed only one win in nine games.
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