Tests revealed Chisholm has a stress reaction in his lower back, the Marlins said Friday. He is expected to miss six weeks.
Chisholm, 24, was selected to the National League All-Star team for the first time in his career. However, he was forced to miss Tuesday's game at Los Angeles.
He has been on the injured list since June 29 with what was called a right lower back strain.
"He was really pushing hard to get to that All-Star Game, so we knew there had to be something more seriously wrong when he couldn't make it," Marlins manager Don Mattingly said before his team played the Pittsburgh Pirates. "Now, it's time to take the steps for him to get it right and go through that process. You feel bad for Jazz. He's having a great year."
Chisholm is hitting .254 with 14 home runs, 45 RBI and 12 stolen bases in 60 games. He leads the team in homers and RBI.