The Ligue 1 champion brings its campaign to a close on Saturday with a trip to Reims but will be without the 23 year-old centre-back.
"Presnel Kimpembe underwent a procedure on his groin on Thursday at the Sports Clinic in Paris," a club statement read. "Led by Dr. Gilles Reboul, the intervention was conducted without problems. His rehabilitation will begin in the next few days."
Kimpembe, a World Cup winner last year, has also been left out of Didier Deschamps' France squad for the upcoming matches against Bolivia, Turkey and Andorra as he looks to recover from his injury problems.