Chisholm had been battling the injury in recent days.
He missed two games before returning Tuesday against the the Cardinals, but was removed in the middle of the second inning with right lower back discomfort.
Chisholm is currently the leading vote-getter among National League second basemen for next month's All-Star Game. He's leading the Marlins with 14 home runs and 45 RBIs this season.
In the corresponding roster move, infielder Luke Williams was recalled from Triple-A Jacksonville.