General manager Frank Wren said Sunday that Freeman's injury will keep him out of the game.
Freeman jammed his left thumb on the first play of Saturday night's 5-2 win over the Cincinnati Reds. Shortstop Andrelton Simmons fielded Chris Heisey's grounder and threw slightly wide of first base, forcing Freeman to catch the ball in Heisey's path. Heisey hit Freeman's glove and was out.
"I guess my thumb was in the wrong place," Freeman said. "It's just one of those freak injuries I seem to run into every year."
Freeman remained in the game. He wore a soft splint on his left hand and is not playing in Sunday's game.
He said there is "a little bit of tiny swelling" in the thumb.
"I can still bend it and do everything," Freeman said. "It's not too bad, so I'm just going to take a day off and see how it goes."
Freeman made the All-Star roster by finishing ahead of Dodgers rookie Yasiel Puig on the fan vote. Freeman will still make the trip to New York for the All-Star game.
Before the decision was made that Freeman will not play in the All-Star game, he said the priority is protecting his health for the NL East-leading Braves.
"I've got to look out for the best interests of this team, so I've got to be available to play in the second half," Freeman said. "If I can't play in the All-Star game, we're better off if I'm able to play in the second half.
Manager Fredi Gonzalez said Freeman can receive treatment for the injury while at the All-Star game.
"I think he needs to go," Gonzalez said. "... You never know when that chance will come again."
Evan Gattis, who had been out since June 18 with a right oblique strain, was activated from the 15-day disabled list and is starting at first base.
Gattis came off the DL after playing only two games in his injury rehabilitation stint with Triple-A Gwinnett. The original plan had been for Gattis to remain with Gwinnett through Sunday.
"It was good," Gattis said of his rehab stint. "I felt good to square up the ball last night. That tells me I'm ready."
Gattis, whose primary position is catcher, has started 11 games in left field and only three games at first base.
B.J. Upton, who left Friday night's game with a right adductor muscle strain, was placed on the 15-day disabled list, retroactive to Saturday.
"We've got a break coming up and I just need a little more time to get healthy," Upton said, adding his recovery "is not a thing that's going to happen immediately."
Justin Upton also left Friday night's game with what was announced as a left calf strain. On Sunday, Gonzalez said team doctors concluded the injury was just a severe cramp.
Gonzalez said Justin Upton would be available in an emergency situation Sunday.
The Braves expect a third injured starting outfielder, Jason Heyward, to recover from his strained right hamstring without being placed on the disabled list.
The Braves' patchwork outfield of Jose Constanza, Reed Johnson and rookie Joey Terdoslavich combined for seven hits Saturday night and is starting again Sunday.