With the win, San Jose (17-6-5) extended its Western Conference lead over Seattle to eight points, while Chivas (7-13-7) is now tied with Portland for fewest in the conference.
Chivas coach Robin Fraser was ejected after the first half ended for arguing with a referee.
San Jose opened the scoring after a delayed penalty kick call. Gordon lay on the ground inside the penalty area for several moments while his teammates continued the attack. After play was stopped in the 19th minute, San Jose was awarded a penalty kick and Wondolowski converted it.
Gordon scored in the 49th off a pass from Wondolowski, who finished the night with 19 goals and seven assists on the season -- both career highs.