The Rapids had two penalties, but a late red card set the stage for Dom Dwyer's injury-time winner.
After a scoreless opening period, the defending champions took a lead early in the second half. Catching Colorado on the counter, Sal Zizzo ran down the right channel before cutting a low cross to Graham Zusi, criminally unmarked on the far post. The U.S. international finished to make it 1-0 in the 50th minute.
Colorado was awarded a penalty in the 57th minute. Eric Kronberg spilled Vicente Sanchez's cross into the box, and in the chaos, Ike Opara fell to ground and struck the ball with his hand. Colorado was awarded its fourth penalty in three games. Sanchez stepped up and although Kronberg put a hand on the shot, it settled in the back of the net just before the hour mark.
The Rapids were awarded yet another penalty in the 77th minute. Nick LaBrocca picked up Benny Feilhaber's poor clearing pass and fed Shane O'Neill in the box. Feilhaber, desperate to atone for his mistake, hauled down O'Neill and conceded the kick, which Sanchez put away with ease.
The lead lasted just seconds, as Feilhaber made up for his mistake. Zusi's long cross was headed into the middle by Zizzo, and although Feilhaber whiffed at his first attempt, he cleaned up with the second to make it 2-2.
The Rapids lost defender Marvell Wynne to a second yellow card in the 86th minute for a rash tackle on Zusi.
With Colorado down a defender, Kansas City found a late winner. From the middle, Zusi moved the ball wide left to Dom Dwyer, and with Drew Moor standing off, the Kansas City forward was able to take a step ahead of the defender and rip a shot past John Berner.
The win is KC's second straight, and takes the defending champions to 2-1-1 for the season. Colorado falls to its first defeat, and is now 1-1-1.