Utley pinch hit on Saturday, a day after being struck by the Mets' Mike Pelfrey, and the Phillies were rained out on Sunday. Manager Charlie Manuel said Utley's foot began to bother him during Monday's 6-1 victory over the Cardinals.
Manuel said Utley told him he could play but "I felt like there was no sense in me taking a chance on it getting any worse. I didn't want him to be down for a long period of time."
Manuel said there was a large knot on Utley's foot.
Miguel Cairo started in place of Utley and batted seventh. He went 1-for-4 in Philadelphia's 10-7 win. Raul Ibanez batted third for the first time this season, going 2-for-4 with a double and scoring one run.
Utley led the Phillies with a .346 average and was tied for the lead with eight homers and 21 RBIs. Manuel said Utley was available to pinch hit, but he did not.
Information from The Associated Press contributed to this report.