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However, the game was turned on its head on 77 minutes when Matias Laba was sent off for a second bookable offence when he handled the ball.
Within moments, Jose Mari got on the end of a Marc Burch pass to put the Rapids back on terms.
Two minutes after their equaliser, the forward put Colorado ahead when he latched onto Nathan Sturgis's accurate delivery to net a second and secure victory.
The result means that the Rapids now leapfrog Vancouver in the Western Conference standings.