Walter Martinez put the Earthquakes (14-11-9) ahead to stay at 1-0 with his second goal of the season in the 27th minute.
Wondolowski doubled the advantage in the 56th with his 11th of year when he blasted in a loose ball with a left foot.
Stephen Keel scored in the 90th for Dallas, which finished the season with an 11-12-11 record.
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