Manager Mike Redmond said initial reports don't show any concussion-like symptoms. But Stanton is receiving further examinations on Wednesday to determine if it is nothing more than a bruise to the back of his neck.
"We're anticipating everything will be fine," Redmond said. "Hopefully, it is. Then he will be right back at them. He's a tough guy. It didn't even drop him."
With the first Grapefruit League game set for Saturday against the Cardinals, the Marlins on Wednesday had pitchers face batters for the first time in a game situation.
The morning was running smoothly until Fernandez, the team's top prospect as ranked by MLB.com, had a fastball get away from him.
"I wasn't dizzy or nothing," Stanton said after being immediately evaluated by the Marlins' training staff. "I saw a little grayness, fuzziness on the outside of my eyes, but it's subsiding now."
Stanton believes he is fine, but to make sure, he is undergoing more tests.
"Going to see doctor," the 23-year-old right fielder said. "We're going to go make sure everything is good. We're going for a quick checkup right now."
Stanton also doesn't believe he will miss any practice time.
"Hopefully, not," the slugger said. "But I would say no."
If there aren't any warning signs on Thursday morning, Redmond isn't ruling out getting Stanton back on the field.
"We'll wait and see how he's doing tomorrow," Redmond said. "See how he is in the morning. If he feels fine, and everything is good to go, then I don't have a problem with him [returning]. Probably the quicker we get him back in the box, the better, after something like that. I've seen guys get hit before. You have a little bit of anxiety. You want to get him back in there as soon as he's able to do that."
Stanton was second in the National League in home runs last year with 37. He is scheduled to play for Team USA in the World Baseball Classic.
After being plunked, Stanton walked to the dugout, where he was observed by Marlins assistant trainer Mike Kozak.
A few minutes later, Stanton walked to a cart, pausing briefly to sign a few autographs. But he was driven back to the clubhouse by Kozak in a golf cart.
Fernandez, too, was shaken by the incident.
"Normally, I've got a lot of control and I throw a lot of strikes," the hard-throwing right-hander said. "That was just one pitch. The ball slipped out of my hands. It went to the wrong side. I'm still worried about it."
A year ago, Fernandez said he hit just two batters with pitches.
When Fernandez returned to the clubhouse, he immediately went to check on Stanton.
Stanton eased the mood by making light of the situation.
"When I asked him how he's doing, he laughed. He said he is fine. I told him, 'I'm sorry,'" Fernandez said. "You know, nobody is trying to hit anybody. Same team and everything. He just laughed, said, 'Bro, it's baseball. It happens.'
"When I saw it, I got nervous. I got nervous, not pitching. I know it was over 95 mph. I know it was. It's a scary moment."
Stanton told Fernandez: "Don't dwell on it. We're good. ... Obviously, you didn't mean to. No big deal."
The incident quieted what was an enthusiastic morning, during which Marlins players first did some drills before playing in a simulated game.
Fernandez had retired the first three batters he faced, all on groundouts, before Stanton stepped to the plate.
Stanton had no time to react.
"It's happened before, and it will happen another time," he said. "It hit me first, and the helmet decided to come in after the impact."
"You worry about Fernandez, too," Redmond said. "How a kid like that, a young kid, responds. He faced him two days ago, and everything was fine. I'm sure he's upset that he hit him. We're all teammates."