Wondolowski, who hadn't scored in league play since May 8, recorded his sixth goal of the season in the 45th minute when Victor Bernardez sent him a header near the 6-yard box.
The Earthquakes forward doubled the advantage in the 87th minute, scoring on the rebound of a Shea Salinas shot.
San Jose (8-9-6) improved to 7-1-4 at home.
Chivas USA (4-12-5), meanwhile, saw its road winless streak extend to 10 consecutive matches.
Swim Week Miami Beach 2014 [PHOTOS]