Alvaro Saboria and Fabian Espindola scored for Real, which is alone atop the Western Conference standings and extended its unbeaten streak against the Rapids to seven games.
It sets up a showdown next week against East leader Sporting Kansas City.
Espindola's goal in the 57th minute put him level with Robbie Findley for Real Salt Lake's all-time lead in MLS goals scored with 29.