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"Steven Sykes and Heinke van der Merwe were calling me a baboon during the scrums last night," Mujati posted on his Twitter feed on Saturday.
"Racism is still alive and things don't change."
Former Sharks lock Sykes and Lions prop Van der Merwe are now based in Ireland, while Mujati plays for Saints.
"I was shocked by how blatant they were being and to think I actually thought I knew Heinke from back in the Lions days," Mujati posted on the social network.
"The guy then tries to shake my hand after the game. Naturally I kindly told him to f*** off.
"I wish them all the best with their careers."
Leinster Rugby said in a statement that there would be a full internal investigation into the matter.
"The managements of both teams are in close communication and hopefully the matter will be resolved as soon as possible," it said.
The Zimbabwean-born Mujati has earned 12 caps for the Springboks, while Van der Merwe has one national cap to his name and Sykes has featured for the Emerging Boks.
Leading up to the announcement of South Africa's World Cup squad on Tuesday, there was talk that Mujati could be a surprise inclusion.
In the last eight months, the big prop forward has gained a tremendous support base at his club with cries of "Mooooooooj!" often emanating from the stands when he touches the ball.
Since joining Saints, Mujati has established himself as one of the best tightheads in world rugby, but issues revolving around his passport took him out the running as a real contender for the World Cup squad.
