Mujati, 26, made the claims via his Twitter account on Saturday in the aftermath of Friday's friendly between the two clubs. Press Association Sport understands Heinke van der Merwe and lock Steven Sykes, the two players named by Mujati, denied the allegations. Mujati later deleted his postings.
In a statement released on Sunday, the Irish club said: "Following the allegations made by a Northampton Saints player in the aftermath of Friday night's friendly between Leinster Rugby and Northampton Saints, Leinster Rugby acknowledge that there was an exchange during the match between two Leinster players which was misinterpreted."
It added: "It was regrettable that any offence was caused. Both clubs have agreed that the matter is now closed and will now focus on preparing for their respective league campaigns."