Bohm missed Sunday's game at Atlanta with tightness in the hamstring, and the Phillies were off Monday. He returned to the lineup Tuesday against the Mets but aggravated the injury making a defensive play at third base.
"Very mild, but we want to take care of it and knock it out," manager Rob Thomson said. "He had the two days off and we thought we had knocked it out."
Bohm, the No. 3 overall pick in the 2018 draft, is batting .265 with six home runs and 37 RBI in 53 games this season.
The Phillies promoted infielder Drew Ellis from Triple-A Lehigh Valley ahead of Thursday's matinee against the host Mets, who have won the first two games in the series.