The tie gave the Rapids (11-13-8) the final playoff spot in the Western Conference.
Thiago Martins scored the other Colorado goal; and net-keeper Joe Cannon made one save.
Colorado was short-handed due to the suspensions of Clint Mathis and Mike Petke.
Craig Waibel scored two goals; Paul Dalglish scored once; and net-minder Pat Onstad made two saves.
The Dynamo (11-8-13), second in the Western Conference, had secured a playoff spot before Saturday's match.
In the first round of the MLS playoffs next Saturday, Colorado is home to Western Conference leader FC Dallas. Houston will be at Chivas USA.