It looked to be a draw before the U.S. national team midfielder scored shortly before the end of regular time.
Benny Feilhaber found the net for the hosts in the 33rd minute, picking up a loose ball in midfield and curling an audacious shot around Clint Irwin from some distance.
Colorado got one back in the 77th, when Edson Buddle's attempt deflected off Matt Besler and wrong-footed Jimmy Nielsen.
But with two minutes remaining, Zusi played hero. Streaking down the flank, right back Chance Myers hit a looping service to the far post. After C.J. Sapong teed him up with a header, Zusi ran onto the pass and fired a shot past Irwin.
With the win over Colorado (10-8-9), Kansas City (12-9-6) moved into a three-way tie with the New York Red Bulls and Montreal Impact for first place in the East.