He was taken out of the lineup less than 20 minutes before the first pitch.
Ehire Adrianza batted leadoff and playing right field in Acuna's spot. He led off the game with a triple to the right-field corner off Mets ace Jacob deGrom and scored on Ozzie Albies' RBI single to tie the game at 1-1.
Acuna did singled as a pinch-hitter in the eighth inning of a game the Braves won, 4-3.
Acuna showed no signs of an injury in Wednesday's 20-2 win over the Mets in which he hit a 447-foot homer.
He leads the National League in runs, ranks second in stolen bases and is third in home runs.
The Associated Press contributed to this report.