Wondolowski converted on a controversial penalty kick in the 40th minute, giving him a league-leading and career-high 19th goal of the season.
The referee's decision to award Wondolowski the kick led to the ejection of Chivas captain Robin Fraser for arguing the call at the end of the first half.
Wondolowski and Justin Morrow set up Gordon's tally in the 49th minute and San Jose improved to 17-6-5, extending its Western Conference lead to eight points.
Chivas fell to 7-13-7.
Swim Week Miami Beach 2014 [PHOTOS]