The 'Quakes forward was needlessly sent off as his team slumped to five games without victory.
The best chance of the game fell to San Jose's Alan Gordon. His header from a corner hit the crossbar and although it rebounded back off his body, Rapids goalkeeper Clint Irwin snatched it up.
Adam Jahn was shown a red card in the 87th minute after a reckless, late barge into Jared Watts. Despite the midfielder having already passed the ball away, Jahn threw his shoulder into the Colorado man's head.
The Earthquakes are now 0-2-3, last place in Major League Soccer's Western Conference. Colorado moves to 3-1-2, second in the West. The Rapids are on a three-game undefeated streak in MLS.