Stanton sustained multiple facial fractures, dental damage and cuts that needed stitches after being hit in the face by a fastball from Milwaukee's Mike Fiers.
The Marlins said Stanton, the major league RBI leader and a top candidate for the NL MVP award, would return to Miami on Friday.
"We do not believe he will require surgery," the team said Friday.
Asked if Stanton could play again this season, Marlins manager Mike Redmond said, "It does not look good."
"It's devastating for us. Devastating. For his season to end like that, I mean, that's not good," Redmond said.
Stanton's father was at Thursday night's game and came onto the field while his son was treated. Stanton was bleeding heavily from his mouth, and was driven away from the plate in an ambulance. His father rode with him to the hospital.
Redmond said Stanton did not lose consciousness. Stanton did not say anything while down on the ground, Redmond said.
"It was very, scary," Redmond said. "We're hoping he is going to be all right."
The outfielder tops the NL with 37 home runs and has 105 RBIs, and is batting .288. Miami has 17 games left this year.
It was ruled that Stanton swung trying to get out of the way of the 88 mph pitch from Fiers. Reed Johnson batted for Stanton and was hit in the hand by Fiers' next pitch, bringing angry players off the Marlins bench. Miami's Casey McGehee and Redmond were ejected.
It was also ruled that Johnson swung at the pitch that hit him, ending the inning with two runners on base.
"I've never seen anything like that and I've definitely never seen two swings called on those two plays," Redmond said. "I've never seen a guy get hit in the mouth and called for a swing. He's out there bleeding at home plate and for the first base ump to say he swung at that pitch, what a joke."
Plate umpire Jeff Kellogg said he consulted with first base umpire D.J. Reyburn and determined that both Stanton and Johnson had swung.
"We've both looked at it and, yes, he did swing. They both did, at those pitches," Kellogg said.
Redmond and Johnson said the benches cleared because of the reaction by Fiers after Johnson get hit. Fiers threw up his hands and looked into the Marlins' dugout.
"He just knocked out our best player, hit him in the mouth and then you just hit another guy in the hand," Redmond said. "What are we supposed to do? No doubt, we're trying to win games, they're trying to win games, but you just hit a guy in the mouth."
Fiers insisted the pitch got away from him. He apologized to Stanton on Twitter after the game and was distraught on the field and in the locker room.
"It was heat of the moment stuff," Fiers said. "I just want to make sure that Stanton is OK. I just want to send my thoughts and prayers and everything to Stanton. You never think of throwing at somebody like that. Never in my life has that happened. I just feel very, very sad that I hit him. I'm sorry to their teammates, their fans, his family. It is just tough."
Miami reliever Anthony Desclafani hit Carlos Gomez in the sixth with a pitch and was quickly ejected by Kellogg. Marlins bench coach Rob Leary was also tossed.
Fiers (6-2) pitched five innings. He is 6-1 since being recalled from the minors to join the rotation Aug. 9. Francisco Rodriguez pitched a scoreless ninth to record his 41st save in 46 chances.
Nathan Eovaldi (6-11) lasted only four innings, giving up four runs and eight hits.
HOME RUN STREAK
Marcell Ozuna hit his 23rd homer in the eighth, a two-run shot. Ozuna homered in his fourth straight game, tying a team record.
Marlins: RHP All-Star Henderson Alvarez is set to return to the mound Friday as he missed his last start after straining his oblique Sept. 1.
Brewers: Braun was back in the starting lineup after not starting the past two games as he nurses a thumb injury.
Marlins: Miami moves on to Philadelphia, where Alvarez (10-6) will face Phillies LHP Cole Hamels (8-7).