A Confederation of African Football (CAF) statement released on Saturday said the Tunis outfit must stage their next two matches in continental competitions without spectators.
The four-time winners of the Champions League - the premier African club competition - have also been fined $300,000. Esperance said they will appeal the sanctions, believing they are "too severe", after clashes between some of their supporters and riot police in Rades near Tunis last weekend.
In a move still to be explained, some spectators tried to invade the pitch at half-time during a quarter-final second leg against Algerian club JS Kabylie.
There had been no goals during the first half, leaving Esperance leading 1-0 on aggregate in the north African showdown. While police prevented an invasion of the pitch, some were injured by various objects hurled at them.