Zenit St Petersburg have been fined $10,000 (£6,130) by the Russian Football Union after one of their fans offered Roberto Carlos a banana.
The incident happened in March before Zenit played the Brazilian's current team Anzhi Makhachkala.
A few days later, Zenit said the fan would be banned for life from the club's Petrovsky Stadium.
In 2008, Zenit were fined $58,000 after fans threw bananas and monkey chanted at black Marseille players.
Carlos, 37, a member of three Brazilian World Cup squads, joined Anzhi Makhachkala this year from Corinthians in Brazil.
Racism among football fans is a problem in Russia, which will stage the World Cup finals in 2018.
Last November, shortly before football's world governing body Fifa chose Russia to host the tournament, the the Russian Football Union adopted a seven-point plan to fight racism.
It includes a commitment to producing anti-racist guidelines and establishing a website called Racism Offside.
But critics will argue the relatively small fine levied against Zenit undermines that commitment.
Zenit are the only major Russian club never to have signed a player of African heritage.
Leading figures in Zenit's 5,000-strong Ultras contingent told the BBC last month that they did not want black players in their team.
One unnamed fan, who is an employee of the club, said: "We don't have a problem with black players. No black players - no problem."
However, club officials have denied that race has any impact on who they sign.
After the incident involving Carlos, Zenit released a statement condemning racial intolerance.