Marlins president Michael Hill made the announcement to reporters during Tuesday night's 7-1 loss in Los Angeles against the Dodgers.
The 21-year-old Fernandez, who won Rookie of the Year honors last season and finished third in the Cy Young voting with a 12-6 record with a 2.19 earned run average, is 4-2 with a 2.44 ERA in eight starts and leads the majors with 70 strikeouts.
"Pitching's a precious commodity and we've always tried to be very careful with it. So you try to err on the side of caution," Hill said.
"We've done everything we've thought was the right thing, as to how we've handled him. It's just one of those things that happened."
The Cuban-born Fernandez, who is on the 15-day disabled list, is weighing his options but season-ending surgery appears likely.
"I'm sure he feels like he's letting his teammates down because he got hurt, and all the things that come with the type of competitor he is," said Marlins manager Mike Redmond.
"But all we really want is for him to be OK and getting himself healthy and getting back to the ball club. That's the important thing."
The rehabilitation period for the reconstructive surgery would range from 12 months to 18 months.
(Reporting by Larry Fine in New York; Editing by Julian Linden)