Gordon, a substitute in the 57th minute, headed in a perfectly placed cross pass off the left wing from rookie midfielder Sam Garza to tie it. San Jose (7-2-2) moved into sole possession of second place in the Western Conference, three points behind Real Salt Lake.
Chivas USA (3-6-1) withstood San Jose’s pressure for nearly the entire afternoon, trying to make a goal by rookie forward Jose Correa in the fourth minute stand up for the winner.
Correa, a 19-year-old Colombian signed by Chivas USA last month, curled a shot to the far post from 7 yards out for his first career MLS goal. Miller Bolanos set James Riley free down the right sideline, where Riley crossed in for Correa to finish.
The Earthquakes dominated possession after that, peppering Dan Kennedy with shots until Gordon broke through.
San Jose held possession for 62.5 percent of the match and had 24 shots, six on goal. Chivas USA recorded just five shots overall, and only Correa’s was on target.
Kennedy made five saves, including a couple of spectacular ones to deny Steven Lenhart in the second half. But Kennedy could do nothing on Gordon’s goal, when the 30-year-old beat the goalkeeper to Garza’s cross at the near post.
That helped San Jose avoid suffering a fourth home defeat in five matches to Chivas USA since being re-established as an expansion side in 2008.