The southpaw's locker in the clubhouse at Citizens Bank Park had been cleaned out before the Phillies' game against the Astros on Wednesday before general manager Ruben Amaro Jr. made the announcement on a conference call late in the day.
"We hope to get him into a throwing program in October or November," Amaro Jr. said, according to MLB.com. "Right now he needs to rest."
Last Thursday, Lee was making his second start after a two-month stint on the DL when he was reinjured.
The 2008 NL Cy Young winner had been placed on the 15-day disabled list with a Grade 2 flexor pronator strain. As of now, he does not need surgery.
The hope is Lee will be fully healthy by spring training. The Phillies owe the four-time All-Star at least $37.5 million after this season.
Information from The Associated Press was used in this report.