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.
Kuban sporting director Sergei Doronchenko was banned for the entire 2011-12 season and assistant coach Nikolai Khlystunov for the rest of the year for their role in the incident.
"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.
Kuban said they had settled the dispute by paying Nikezic compensation of $294,000 for the final year of his contract.
