The Brewers slugger grounded out in his first two at-bats. He was replaced in the fifth by pinch hitter Elian Herrera, who stayed in the game in right field.
The Brewers lost 5-4 after the Braves staged a late comeback starting in the bottom of the sixth.
Braun returned last week from a stint on the 15-day disabled list with a right oblique strain. He is hitting .289 overall with seven homers and 19 RBIs.
The Brewers also were without center fielder Carlos Gomez on Thursday. He is day to day with ongoing lower-back issues.
Information from The Associated Press was used in this report.