San Jose (2-1-1) beat Seattle (0-2-1) for the fourth straight time in regular-season play, building on a sweep of three contentious meetings last year.
It was the second score this season for Wondolowski, who tied MLS' career record with 27 goals last season - including two winners against Seattle.
Wondolowski brought down a long pass that skidded off the head of Seattle defender Jhon Kennedy Hurtado at the edge of the Sounders' penalty area. Wondolowski's touch was gentle enough that he ran onto the ball for a 22-yard strike that curled around Seattle's sliding Djimi Traore. The ball barely escaped the reach of Seattle goalkeeper Michael Gspurning before ricocheting in off the far post in the 46th minute.
Gspurning kept San Jose from adding an insurance goal with a stop on Shea Salinas' redirection shot in the 61st minute.
San Jose goalkeeper Jon Busch made two critical saves in the 75th minute, diving to stop Mauro Rosales' half-volley from the top of the box, then scrambling to deflect David Estrada's rebound attempt at point-blank range.
The Earthquakes narrowly avoided disaster in the 84th minute when Ty Harden's back pass came up well short. But Estrada appeared to overrun to ball some 35, perhaps spooked by an onrushing Busch.
Busch plucked a swerving long-range free kick from Osvaldo Alonso in the 89th minute to stifle Seattle's last chance.