Dillon Powers' smart finish in the area and a penalty from Vicente Sanchez saw Colorado defeat Vancouver Whitecaps 2-0 in Denver and, after Real Salt Lake lost 1-0 at Chivas USA, the Rapids secured second spot in the West's standings.
Colorado (25 points) lead Real on games won, although they remain well behind leaders Seattle Sounders (35), who triumphed 1-0 at DC United on Saturday thanks to Chad Barrett's first-half goal.
At Dick's Sporting Goods Park, the Rapids deservedly took the lead in the 20th minute when Powers produced a clever turn in the box, after controlling Marvell Wynne's deflected cross, and the 23-year-old forward smashed his left-footed shot past Vancouver goalkeeper David Ousted.
With nine minutes remaining in the first half, Whitecaps defender Nigel Reo-Coker conceded a penalty when he blocked Deshorn Brown's run and Sanchez made no mistake from the spot.
Colorado almost led 3-0 at the break but Ousted made a good save to stop Sanchez's bicycle kick.
The second half rarely got going, which suited Rapids coach Pablo Mastroeni, although Colorado goalkeeper Clint Irwin was forced into two smart saves to ensure a clean sheet.
The victory made it three wins and a draw in Colorado's past four MLS games at home, although they did lose to the Atlanta Silverbacks in Denver on Tuesday in the US Open Cup.
In California, Real's terrible form continued as they missed an opportunity to regain second position in the Western Conference.
The Utah-based club had midfielder Luke Mulholland sent off after just eight minutes at the Stubhub Center for a raising a boot as he slid in on Martin Rivero right in front of the referee.
Chivas dominated the match from then on and Erick Torres struck the only goal of the game 10 minutes before half-time, thrashing a volley into the net from Tony Lochhead's cross-field pass.
The result extended Real's winless streak in all competitions to six games.
In the California Clasico, Gyasi Zardes scored just after the hour mark to give Los Angeles Galaxy a 1-0 triumph over San Jose Earthquakes, while in the other MLS game, Philadelphia Union defeated New England Revolution 3-1.
Columbus Crew versus FC Dallas was called off after a fan of the former club was reportedly struck by lightning outside the stadium in Ohio.
