Former Montenegro international Nikezic said he had been forced to terminate his contract with the Premier League newcomers after being beaten up and threatened with a gun.
The RFU said on its website that Kuban had been fined two million roubles ($70,570), while the club's general director Suren Mkrtychan would have to pay one million roubles.
"We could not prove that Nikezic had suffered any physical force but it's a fact that the contract was annulled against the rules," said the RFU ethics committee chief Alu Alkhanov.
Last month, Nikezic lodged a complaint with FIFA and UEFA saying he had been beaten up and threatened with a gun at Kuban's training ground, forcing him to annul the final year of his two-year deal with the club.
"I was invited into a room where I was met by two strong men," Nikezic wrote in a letter to football's world and European governing bodies.
"When I refused to sign, saying I still have another year on my contract, I received a powerful blow to the liver. I simply feared for my life," added the 29-year-old, who represented Serbia & Montenegro at the 2004 Athens Olympics.
