San Jose, playing down a man after Steven Lenhart's red card in the 81st minute, went ahead when Alan Gordon launched a long shot from outside the penalty area that Chivas goalkeeper Dan Kennedy made an initial stop on.
But Kennedy couldn't control the rebound and coughed it up right to Wondolowski, who easily put it past him for his ninth goal of the season.
The Earthquakes (12-11-8) stayed in the Western Conference playoff hunt, pulling within one point of fifth-place Colorado.
Last-place Chivas fell to 6-18-8.
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