Freeman, who was voted into the game by fans, hurt his thumb on Saturday against Cincinnati and missed the team's final game before the break.
He will be replaced on the All Star squad by Braves team mate and catcher Brian McCann, who was chosen by National League manager Bruce Bochy.
"It's unfortunate that (Freeman) won't be able to play in the game, but I'm happy to be going in his place," McCann told the Braves website. "I'm glad someone in this clubhouse got to go in his place."
Freeman will still make the trip to New York for the game, his first All Star selection, while McCann is receiving the honor for a seventh time.