An All-Star last season, Cook is 10-6 with a 4.47 ERA in 25 starts. To replace him on the roster, Colorado purchased the contract of right-handed reliever Matt Herges from Triple-A Colorado Springs.
The Rockies began the day leading the NL wild card race by one game over San Francisco.
Cook was hurt during Friday night's 6-3 loss to the Giants. Rockies manager Jim Tracy said Cook felt something in his shoulder during a four-pitch walk to Nate Schierholtz to start the fourth inning. Cook motioned to the dugout after the walk and was taken out after being looked at by trainer Keith Dugger.
Tracy said Cook will have an MRI on Monday and the early signs are encouraging that it won't be a serious injury.
This is Cook's first trip to the DL since 2007, when he missed the last seven weeks of the regular season with an oblique strain. He returned to pitch Game 4 of the World Series against Boston.
The Rockies signed Herges on July 17, eight days after he was released by Cleveland, where he was 2-1 with a 3.55 ERA in 21 appearances. Herges was assigned to Colorado Springs, where he was 3-2 with a 1.96 ERA in 13 appearances.
Herges was with the Rockies for the previous two seasons, including 2007 when he was 5-1 with a 2.96 ERA in 35 games for the NL champions.
To make room for Herges on the 40-man roster, the Rockies transferred reliever Manny Corpas from the 15-day DL to the 60-day DL.