The 25-year-old was acquired from the Blue Jays in exchanged for minor league right-hander Chris Malone. Toronto will also receive a player to be named or cash considerations to complete the trade.
Emaus will not be added to Colorado's 40-man roster and is set to report to Triple-A Colorado Springs.
After selecting him in the Rule V Draft before this season, the Mets named Emaus their Opening Day second baseman. But he struggled in the big leagues, hitting .162 in 42 plate appearances before they decided to return him to the Blue Jays on Thursday.
Malone was originally drafted by the Royals in the 36th round of the 2003 First-Year Player Draft. After spending some time in independent ball, Malone joined the Rockies organization in 2008. The 27-year-old reliever went 3-5 with a 4.10 ERA for Double-A Tulsa last season. He was 1-0 with a 4.15 ERA at the time of the trade.