Zenit St. Petersburg was fined 300,000 rubles ($10,620) for a racist incident targeting former Brazil fullback Roberto Carlos in a league match last month.
A fan was seen offering a banana to the Anzhi Makhachkala captain at St. Petersburg's Petrovsky Stadium before Zenit's home league opener. Zenit won the game 2-0.
The Russian Football Union's disciplinary committee found Zenit guilty of "a racist insult and disorderly conduct," the RFU said on its web site.
The committee also fined Dynamo Moscow 300,000 rubles after their fans rioted during Saturday's league match at Volga Nizhny Novgorod. Volga was fined 200,000 rubles.
It was the latest in a series of football-related incidents in Russia, which will host the 2018 World Cup.
Violence and ethnic tension was on the agenda at a meeting by government officials on Wednesday when Prime Minister Vladimir Putin urged the Russian Football Union to work with fan groups to ensure a peaceful tournament in 2018.
"We've promised FIFA, the world and sporting communities that Russia will hold the tournament under the principles of tolerance and goodwill," Putin told officials responsible for organizing the 2018 event. "And these basic principles must be followed without any doubt or compromise."