Matias Perez Garcia added two assists for the Quakes (7-5-4), the first on a well-placed cross that Wondolowski smashed into the net in the 28th minute for a 1-all tie. Wondolowski moved alone into second place the MLS goal race, three behind Columbus' Kei Kamara.
Clarence Goodson gave San Jose the lead in the 53rd minute, heading home Perez Garcia's corner kick.
Cordell Cato capped the scoring for the Earthquakes with a patient left-footed finish in the 72nd.
The Galaxy (7-6-7) took the lead in the 17th minute on Juninho's 30-yard rocket from straightaway that curled just enough from San Jose goalkeeper David Bingham's diving reach.