Dr. Neal ElAttrache performed the 30-minute debridement procedure at Kerlan-Jobe Surgical Center. The club announced that the surgery went as expected.
The 36-year-old Lilly, signed through 2013, had not pitched since May 23 in Arizona, when he walked five and couldn't get out of the fourth inning.
But prior to that he was 5-0 with a 1.79 ERA, off to the best start of his career and in the conversation for an All-Star berth.
Lilly underwent a similar shoulder cleanup operation Nov. 3, 2009, and spent the first three weeks of the 2010 season on the disabled list while making two Minor League rehab starts before being activated by the Cubs. He was traded to the Dodgers on July 31, 2010.