The Earthquakes won for the third time this season and jumped into a fourth-place tie with Los Angeles in the Western Conference.
Walter Martinez received a corner kick for San Jose and headed the ball to Wondolowski, who powered a shot past Joe Bendik into the bottom-right corner of the net.
Wondolowski also assisted on a goal by Adam Jahn in the 48th minute that brought the Earthquakes back from a 1-0 deficit. The Toronto goal came from Justin Braun in the 14th minute.
San Jose climbed to 3-3-5 while Toronto slipped to 1-5-4.