The Earthquakes took the lead in the 18th minute through Chris Wondolowski's 11th goal of the season, but his strike was canceled out in the second-half with equalizer from Drew Moor.
A Khari Stephenson shot from distance bounced directly in front of Colorado goalkeeper Matt Pickens, who failed to hold onto possession of the ball. Wondolowski followed up the shot and stuffed the rebound into the net to give San Jose the lead.
Colorado pushed for an equalizer throughout the second half, and eventually found one 20 minutes from time.
A Rapids corner kick eventually fell to Jeff Larentowicz following a scramble in the box. His shot was initially saved by 'Quakes keeper Jon Busch, but Moor flicked the rebound into the goal to tie the match.
The result is a step in the right direction for the Rapids, as it broke a three-game losing skid and moved them a point closer to fourth-place FC Dallas. It is the second consecutive draw for the 'Quakes, who are winless in their last three matches.
Colorado (10-9-12) sits in fifth place in the West with 42 points, while San Jose (6-11-13) remains in eighth place with just 30 points.
Both teams return to action on Oct. 1 with home matches, as San Jose hosts Sporting Kansas City and Colorado welcomes FC Dallas.