The 22-year-old was replaced by Eric Hinske at first base after he sustained a left index finger contusion. He is day to day.
"He got examined by Dr. [Daniel] Kanell," Braves manager Fredi Gonzalez said. "He put him in a splint and did some treatment, and we'll get an X-ray tomorrow."
The Braves do not know the severity of Freeman's injury, because they could not perform an exam due to a lack of an X-ray machine at Marlins Park.
"We can't tell," Freeman said of the severity of his injury. "Obviously it doesn't feel good. Tomorrow I'm going in the morning to go see a hand specialist."
With the Braves leading, 1-0, a sliding Freeman was hit in the left hand by Jose Reyes' throw to first as the Marlins shortstop tried to turn a double play in the fourth inning.
Because of the interference, Jason Heyward was ruled out at first and Dan Uggla was not allowed to score from third.
"I slid normal and he came with the sidearm throw," Freeman said. "I couldn't believe that call, but that's whatever. I slid normal and didn't do anything different. I wasn't trying to interfere with anything. My hand was in the wrong place at the wrong time."
Uggla eventually scored on a Randall Delgado single, but Freeman went into the clubhouse with the Braves trainer and Hinske replaced him at first when the Marlins came up to bat in the bottom of the fourth.
The injury adds to what has been a very frustrating season for Freeman. After dealing with eye problems for much of the year, he was finally feeling better at the plate.
"I just finally started to feel good with my eyes and started to see the ball, and then seven at-bats later, here we go again," Freeman said. "It's just been an up-and-down season so far, but hopefully this isn't bad. We'll find out in the morning."