Recovery time for Bowen, who turns 30 in March, is expected to be six months. Bowen's rehab could determine if the Redskins need to add to their defensive line in the offseason.
"Hopefully this microfracture will help him, and when he does come back he'll come back full speed," Redskins coach Mike Shanahan said. "You just keep your fingers crossed. It's always tough going through rehab.
"Our guys do it all the time. Stephen is a worker and it's always unfortunate to have a surgery like that. But he's young, he's a worker, so I'm sure he'll bounce back very quickly."
Bowen originally tore the posterior cruciate ligament in his knee during a win against the Chicago Bears on Oct. 20. He reinjured the knee three weeks ago at Philadelphia and was placed on injured reserve Nov. 26.
Bowen failed to make an impact this season. Despite being solid against the run, Bowen failed to record a sack. The Redskins likely will continue to start Kedric Golston at right end with Chris Baker also playing the position.