With the score tied 1-1 in the 30th minute, center back Victor Bernardez found a wide-open Wondolowski with a pass and the Earthquakes striker tipped it past Seattle goalkeeper Michael Gspurning.
Simon Dawkins also scored for the Quakes (18-6-6), who own the league's best record and swept their three-game season series with the Sounders.
Steve Zakuani tallied for Seattle (13-7-9), which fell into fourth place in the Western Conference, one point behind Real Salt Lake and the LA Galaxy.
The Sounders have a game in hand on each, however.
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