Marvin Chavez added his second goal of the season 95 seconds into the game for San Jose (19-6-7). The Earthquakes hold a six-point lead over idle Sporting Kansas City for the Supporters' Shield.
San Jose tied a club with 64 points in a season.
Andre Akpan scored on a penalty kick in the 90th minute for the Rapids.
Colorado (9-19-4) has won only twice in its last 16 games, going 2-11-3 in that span. The Rapids will miss the playoffs for first time since 2009.