Acuna, an All-Star outfielder for the NL East leaders, was pulled before the fifth inning after failing to run out a drive off the right field wall in the third. The ball bounced off the wall for a long single. Acuna likely would have had an easy double if he had hustled from home plate.
Manager Brian Snitker followed Acuna into the tunnel for a conversation during the fourth inning before Adam Duvall entered the game in left field in the fifth, with Rafael Ortega moving from left to center field.
"He didn't run. You've got to run,'' Snitker said. "It's not going to be acceptable here. As a teammate you're responsible for 24 other guys. That name on the front is a lot more important than the name on the back of that jersey. You can't do that. We're trying to accomplish something and do something special here and personal things have got to be put on the backburner. You just can't let your team down like that.''
Snitker also said Acuna handled his decision maturely and "knew he screwed up." Acuna is expected to be back in the lineup for the Braves' next game Tuesday against the Marlins.
Acuna, 21, said through a translator that there was "no excuse" for the baserunning mistake and that he respected Snitker's decision.
Acuna said he "obviously wasn't thinking and that was the action I took. ... It's never happened before.''
The move by Snitker came in the decisive game of a three-game series between the teams with the National League's best records. The Braves trailed 3-1 when Acuna was pulled, but Ortega's sixth-inning grand slam lifted Atlanta to a 5-3 victory.
Acuna just missed robbing Cody Bellinger of a three-run homer in the first with a leaping try in center field.
Acuna is hitting .296 with 35 home runs and 85 RBIs, and he leads the NL with 29 stolen bases and 104 runs scored.
The Associated Press contributed to this report.