Colorado advanced to the Eastern Conference final after Brian Carroll's penalty kick at the end of the fifth round sailed over the goal, giving the Rapids the win.
The Crew won the game 2-1, but the aggregate was tied 2-2 after Colorado won the first game 1-0 at home on Oct. 28. The Rapids host San Jose in the single-game Eastern Conference final on Nov. 13.
The Rapids won the penalty kick shootout 5-4.
Colorado's Conor Casey scored in the 84th minute made it 2-1 and evened the series. Eddie Gaven put Columbus ahead 1-0 in the game in the 22nd minute. Robbie Rogers then gave the Crew the series advantage with a strike from 12 yards in the 70th minute.