San Jose (12-11-8) moved to within one point of Colorado and the Galaxy, which are tied for the fifth and final playoff spot in the Western Conference, with three games to play.
The schedule works in the Earthquakes' favor because their next two games are against Colorado (Oct.9) and the Galaxy (Oct. 20) before they finish at home against FC Dallas.
Steven Lenhart was ejected in the 81st minute and San Jose finished the match with 10 men. Lenhart picked up his second yellow card for a reckless challenge on Chivas goalkeeper Dan Kennedy.
Down a player, San Jose pressured Chivas and was rewarded. With three minutes remaining, Alan Gordon took a shot on goal from the top of the penalty area that Kennedy stopped, but Wondolowski knocked in the rebound for his ninth goal of the season.
Last-place Chivas faces the Galaxy next Sunday.