The outfielder, second in MLB for home runs hit this season, was hit in the left cheekbone by a Mike Fiers fastball during the Marlins' 4-2 loss to the Milwaukee Brewers.
A bleeding Stanton was carted off Miller Park and to hospital after the incident during a clash which featured multiple ejections and delays.
The Marlins said Stanton would return to Miami on Friday for further evaluation, but confirmed multiple injuries.
"UPDATE: Giancarlo suffered facial lacerations requiring stitches, multiple facial fractures dental damage after being hit by a pitch," they said in a tweet.
Tweeting to Stanton, Fiers apologised to the 24-year-old and wished him a speedy recovery.
"I am deeply sorry about what happened tonight. I can't imagine what you and your family are going through," Fiers tweeted.
"My thoughts and prayers are with you at this time. I feel horrible and hope for a speedy recovery."
Stanton's absence would be a blow for the Marlins, who are chasing a wildcard in the National League.
They sit 5.5 games behind the Pittsburgh Pirates late in the campaign.