Harris, 27, joined the Whitecaps after being selected in the second-round (fourth overall) of the 2010 MLS Expansion Draft.
In two seasons with Vancouver, the native of Basseterre, Saint Kitts and Nevis, scored two goals and added three assists in 12 MLS regular season appearances.
"We are thankful for the contributions Atiba made during his two years in Vancouver and wish him all the best with Colorado," Whitecaps president Bob Lenarduzzi said in a statement. "Atiba scored a memorable goal during our inaugural match and although his time on the pitch was limited because of injuries, he was always a great ambassador for the club."
The Whitecaps have 11 international roster spots through the 2013 season and 10 international roster spots through the 2016 season.
Vancouver also exercised the 2013 contract options on goalkeeper Brad Knighton, defenders Jordan Harvey, Greg Klazura, Young-Pyo Lee, and Carlyle Mitchell, midfielders Gershon Koffie, Jun Marques Davidson, and Matt Watson. At the same time, the Whitecaps declined next year’s options on midfielders Michael Nanchoff and John Thorrington.