Simon Dawkins scored his eighth goal of the season in the second minute for the Earthquakes (18-6-6), who won all three matchups against Seattle this season, including two on the road.
Steve Zakuani tied the score for the Sounders (13-7-9) in the 14th minute with his first goal since returning to action in early July after a year-long recovery from a broken leg.
Wondolowski then got the winner in the 30th minute, converting after a corner kick was settled by Victor Bernardez, who passed it into the 6-yard box for Wondolowski's easy tap-in past goalkeeper Michael Gspurning.
No other player in the league has more than 14 goals.
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