Barnes was eligible to return from health and safety protocols on Friday before the knee issue popped up.
The first-round pick hasn't played since Dec. 18. Barnes is averaging 15.6 points and 8.3 rebounds this season.
D.J. Wilson was added to protocols before the game on Friday, joining Isaac Bonga.
Fred VanVleet, OG Anunoby, Khem Birch, Precious Achiuwa and Justin Champagnie all return from protocols for the game versus the Clippers.