Stanton's injuries required stitches to repair facial lacerations, and he lost some teeth.
"He is being evaluated by our team doctors," manager Mike Redmond said. "He is set to see a dentist. I texted him this morning. I know he's feeling better and is on the road to recovery."
Stanton, accompanied by his father, Mike, and Marlins trainer Sean Cunningham, flew on team owner Jeffrey Loria's private plane to Miami.
On Friday, Stanton tweeted: "The amount of support I have received from you guys has been tremendous & Heartfelt. I'm much better today & deeply appreciate your prayers!"
On Friday night, the Marlins opened a three-game series at Philadelphia, and it marked the first game of the season without Stanton.
Neither Stanton nor the Marlins have ruled out the two-time All-Star returning this season. But it appears a real long shot.
"He wants to come back," Redmond said. "We haven't set a timetable on it. It's probably to be determined."
With Stanton out, the Marlins plan on using several options in right field. First baseman Garrett Jones could get some time in right, with Justin Bour playing first. Enrique Hernandez also is an option to play center field, moving Marcell Ozuna to right.
Stanton was hit in the face by an 88-mph Mike Fiers fastball in the fifth inning of Thursday night's 4-2 loss to the Brewers.
The Marlins also expressed their appreciation to the Brewers for their medical treatment of Stanton's injury.
In a tweet, the club said: "Special thank you to the Milwaukee Brewers medical staff & their emergency medical personnel, as well as the Marlins athletic training staff."
A National League MVP Award candidate, Stanton made it clear he hoped to play in all 162 games. Stanton paces the NL in home runs (37) and RBIs (105), posting a line of .288/.395/.555.
"This is a season he was putting up some crazy numbers," said reliever A.J. Ramos, Stanton's roommate. "We see how hard he works on and off the field, and how hard he prepares for every game. Living with him, it's really hard to come to the locker room and he's not here. You feel badly about it. Hopefully we can move forward from here."