Wondolowski's goal during first-half stoppage time came when he collected the ball after a deflection off Seattle defender Jhon Kennedy Hurtado and unleashed a shot from 22 yards that beat goalkeeper Michael Gspurning.
The Earthquakes (2-1-1) notched their fourth straight regular-season win over Seattle stretching back to last season, and moved into a second-place tie in the Western Conference with seven points.
The Sounders fell to 0-2-1.
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