St Petersburg fans made monkey noises at Lokomotiv's black players during Saturday's match, which Zenit won 2-0 to virtually seal their second consecutive Russian league title. They lead CSKA Moscow by 11 points with six games remaining.
Zenit's fine was small compared to the $17,000 imposed on Spartak Moscow's Nigeria international Emmanuel Emenike last month for an offensive gesture he made towards Dynamo Moscow fans who racially abused him during a match.
Emenike also received a suspended sentence until the end of the season. Spartak have appealed the striker's fine.
The Zenit case was the latest in a series of racist incidents in Russian soccer.
In March, a banana was thrown at Anzhi Makhachkala's Congolese defender Christopher Samba in a match at Lokomotiv Moscow. Another Anzhi player, Brazilian full back Roberto Carlos, had bananas thrown at him at stadiums in St Petersburg and Samara last year.
In a separate incident, Zenit striker Alexander Kerzhakov escaped punishment following his collision with Spartak goalkeeper Andriy Dykan last month, which left the Ukraine international with broken bones in his face and a concussion.
"After thoroughly examining the video, the disciplinary committee (KDK) had felt Kerzhakov should not face any sanctions because he didn't have any intent to injure his opponent," KDK head Vladimir Katkov said.
Dykan has had successful surgery in Germany, Spartak said on their website on Wednesday. The keeper will miss the rest of the season.