Fans of the 26-times Bulgarian champions brandished a racist banner and insulted the visiting team's players during the July 19 game which Levski won 1-0, before losing the tie 3-2 on aggregate.
The banner also praised Ratko Mladic, ex-commander of the Bosnian Serb army, and Zeljko Raznatovic, the commander of Serb paramilitary unit "The Tigers", who participated in wars in Bosnia and Croatia in the 1990s.
Levski, who will mark their 100th anniversary next year, urged their fans to behave to avoid further sanctions in future.
"Fans should realise that the club is responsible for all of their extreme or irrational actions," Levski said in a statement.
- Ratko Mladic