Rollins flied out while leading off for the Phillies at Atlanta.
Manuel pulled Rollins on Thursday after a pair of baserunning mistakes in the sixth inning against the New York Mets. The three-time All-Star didn't run hard on a popup that was dropped for an error and later was caught in a rundown.
Manuel met with Rollins before the game against the Braves.
"He said he was wrong," Manuel said. "He apologized to me."
Rollins acknowledged the mistakes and added that he meant no disrespect to Manuel or his teammates.
"You break the rules, that was the punishment," Rollins said. "It's really that simple."
It marked the second time Rollins' lack of hustle was called into question. After a game at Miami earlier this year, Manuel summoned Rollins to his office for jogging down the line on a grounder.
Though he didn't bench Rollins after the first blunder, Manuel had seen enough on Thursday.
"I don't want to try to have to make Jimmy run," Manuel said. "I want Jimmy to want to run, and I want Jimmy to want to run because you're supposed to run and you should run. That's what baseball's all about. I told him the same thing."
Rollins was jogging when Mets pitcher Jonathon Niese dropped a routine pop.
Rollins is a three-time Gold Glove winner and was the 2007 NL MVP. The 33-year-old star leads the team this year in hits, runs, total bases and games.