Jimmy Rollins, who was activated Monday, hit in Utley's No. 3 spot in the order.
Manager Charlie Manuel said Utley had been playing through some illness for the past few days but hadn't mentioned it to anybody.
"He hadn't said anything about it," Manuel said. "He'd been feeling ill the past couple of days. He didn't say too much about it."
Utley hit .333 with a home run and four RBIs during the team's six-game road trip. Monday was just the second game he's missed this season.