The team described Chatwood's injury as a mid-back strain. He leads the Rockies with eight wins this season.
Chatwood threw 48 pitches, the last of which sailed to the backstop for his third walk. A trainer then went to the mound, accompanied by manager Walt Weiss, and after a brief conversation with Chatwood, he left the game.
The Rockies lost the game to the Marlins 9-6.
His start against Miami on Saturday was just his 14th since he underwent his second Tommy John surgery in April 2014.
Chatwood faced 11 batters, got five outs and was charged with three runs before being replaced by Eddie Butler.
Butler, who is 2-4 with a 6.26 ERA and has made seven starts this season, is likely to take Chatwood's place in the rotation.
The Rockies called up right-hander Scott Oberg to take Chatwood's spot on the roster.
Information from The Associated Press was used in this report.