The two-time All-Star pitcher has battled back problems and shoulder inflammation since July and was scratched from a start last week.
"It's the smart thing to do," Johnson told the team's website (florida.marlins.mlb.com). "I had a little bit of it going on in the beginning of the year, and (hoped) that it would go away. It's not fun being on the sideline."
The top performer on Florida's rotation this year, Johnson finished with an 11-6 record, a 2.30 ERA and 186 strikeouts.
Johnson underwent reconstructive arm surgery in 2007 but recovered quickly and earned selections to the National League's All-Star team in 2009 and 2010.
(Reporting by Jahmal Corner in Los Angeles; Editing by Frank Pingue)