Howard originally was in Saturday's starting lineup but was a late scratch. The three-time All-Star has struggled while playing through the knee injury, batting .266 with 11 homers and 43 RBIs this season.
Phillies general manager Ruben Amaro said Howard would have an MRI on Sunday or Monday.
"It got to the point where it's time for him to get off of it, the discomfort is too great," Amaro said. "This is a big blow to us."
The Phillies called up Darin Ruf from Triple-A Lehigh Valley to take Howard's place. Ruf batted .266 with seven homers and 46 RBIs at Lehigh Valley. He had two homers and nine RBIs in 57 at-bats for the Phillies last season.