Wondolowski's fourth goal of the season came after San Jose forward Steven Lenhart drew the penalty in the 24th minute when he was jostled by Seattle's Marc Burch while in the box awaiting a Marvin Chavez cross.
Wondolowski put the ensuing kick past Sounders goalkeeper Michael Gspurning and the Earthquakes (3-1-0) notched their ninth point in four games to start the season.
Seattle (2-1-0) had its best chance in the 84th minute when Fredy Montero's left-footed shot sailed just wide.
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