Manuel found out Friday morning after a meeting with his staff before the game against the Los Angeles Dodgers.
Manuel watched batting practice from his customary spot behind the cage, but did not talk to the media and his usual pregame press conference was canceled. He declined to meet with the media after the game.
Winning pitcher Brett Myers said he told Manuel before the game he was going to win in her memory.
"He's been so good to us," Myers said. "We've got to show him some love, too. My thoughts and prayers go out to his family dealing with this time."
Phillies center fielder Shane Victorino found out after the game that his grandmother died Friday morning. He hopes to attend the funeral in Hawaii, but doesn't want to miss any games.
Manuel wrote of June Manuel for a Mother's Day tribute on MLB.com in 2005: "I can't imagine a better person in the world than my mother. I hope everybody's mom is like mine. She's been very special to me, and I've been very lucky to have a mother like her."
Dodgers slugger Manny Ramirez, whom Manuel managed in Cleveland, was among the players and coaches who stopped to offer condolences. Dodgers manager Joe Torre put a hand on Manuel's shoulder as the two chatted, and former Phillies closer Mitch Williams also dropped by behind the cage.
June Manuel still lived in Buena Vista, Va., where the Phillies manager was raised. She is survived by 10 children. Funeral arrangements were pending.