Just before the break both sides had great chances. First Irwin did well to deny a Wondolowksi dipping effort, while at the other end Atiba Harris saw his shot smack the post.
After half time, Irwin was in the action again, this time to deny Walter Martinez as he tipped his dipping volley over the bar with a great one-handed save.
San Jose finally got themselves level when Marvin Chavez's free kick swerved at the last moment and flew into the top corner past Irwin from 35 yards out.
Minutes later Colorado almost regained their lead when Sturgis met Rivero's corner, but his header clattered off the bar and Busch claimed the ball at the second attempt.
Colorado could have won the game in dying minutes when Deshorn Brown latched onto a long ball from the back and ran towards goal, he tried to lift the ball over Busch but the keeper got a hand to it to tip his effort over.
The Rapids ended the game with 10 men when O'Neill was sent off for a foul on Wondolowski, but the Earthquakes didn't have time to capitalise as both sides settled for a point.