The 20-year-old right-hander hit All-Star slugger Giancarlo Stanton on the back of the helmet with a pitch during a simulated game at the Roger Dean Stadium complex in Jupiter, Fla.
"Normally, I've got a lot of control and I throw a lot of strikes. That was just one pitch," Fernandez told MLB.com.. "The ball slipped out of my hands. It went to the wrong side. I'm still worried about it."
Marlins manager Mike Redmond reported that Stanton would undergo additional tests, although he did not exhibit any concussion-like symptoms.
For his part, Stanton told MLB.com, "I wasn't dizzy or nothing. I saw a little grayness, fuzziness on the outside of my eyes, but it's subsiding now."
Fernandez, the Marlins' top prospect, visited Stanton when he returned to the clubhouse, where the 23-year-old outfielder assured him all was well.
"When I asked him how he's doing, he laughed. He said he is fine. I told him, 'I'm sorry,'" Stanton said. "You know, nobody is trying to hit anybody. Same team and everything. He just laughed. 'Bro, it's baseball. It happens.'"
Fernandez retired the first three batters he faced before plunking Stanton.
"You worry about Fernandez, too. How a kid like that, a young kid, responds," Redmond said. "He faced him two days ago and everything was fine. I'm sure he's upset that he hit him. We're all teammates."
MLB.com's No. 7 overall prospect was one of the breakout stars in the Minor Leagues last season, compiling a 1.75 ERA over 134 innings between Class A Greensboro and Class A Advanced Jupiter. He went 14-1 and compiled 158 strikeouts while issuing only 35 walks.
Fernandez pitched at the Futures Game in Kansas City last summer and was named the Marlins' Minor League Pitcher of the Year.
The Cuba native was selected 14th overall in the 2011 Draft.