Team president Michael Hill made the announcement in the Dodger Stadium press box during Tuesday night's game against Los Angeles.
"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 21-year-old Fernandez is 4-2 with a 2.44 ERA in eight starts. Last season's NL Rookie of the Year was examined Tuesday by Marlins team physician Lee Kaplan in Florida.
Fernandez would be the latest star pitcher in the majors to have Tommy John surgery this year. The recovery time for the elbow ligament transplant procedure can be 12 to 18 months.
The Marlins put their Cuban ace on the 15-day disabled list Monday.
"I think like any 21-year-old kid who hasn't had an injury or been hurt, it's tough," manager Mike Redmond said.
"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. But all we really want is for him to be OK and getting himself healthy and getting back to the ballclub. That's the important thing," he said.
Fernandez is visiting with his family to talk about his options with surgery looming.
"He didn't really give us an idea of when," Hill said. "Obviously, a lot has gone on the past few days, so for him it's a lot to take in and a lot to absorb. So he's just taking the time to digest all the information he's been given from both doctors."
"From what the doctors saw, they did not want to go the rehab route. They felt like surgery was the best option, and that was the recommendation. Hopefully, we can make that call and get things set up and get it taken care of so we can get him on the road to rehab," he said.
Right-hander Anthony DeSclafani will be promoted from the minors and start Wednesday night in his major league debut.
"He's a guy that's done well in the minor leagues and we felt like he was probably the most ready to make the start," Redmond said.
"If we didn't have to use (Kevin) Slowey and (Brad) Hand so much on this road trip, maybe one of those guys would have gotten the start. But we've had to use them a lot, so we really needed a fresh arm. So that definitely played into it."
The 24-year-old former University of Florida star was 3-4 with a 4.19 ERA in eight starts at Double-A Jacksonville.
"Out of all of our younger guys, he's probably a little more polished because he's a college guy and he's got a few more innings under his belt, as far as experience," Redmond said. "There's no doubt that losing Jose is a big blow, but it's also an opportunity for guys to step up and show what they can do."