The August 18 game in Sousse was called off in the 69th minute after home fans invaded the pitch while others threw missiles including stones, bottles and firecrackers, the Confederation of African Football said in a statement.
It is the first time a club has been expelled in the middle of the group stage.
Etoile fans swarmed on to the pitch after bitter rivals Esperance had taken a 2-0 lead.
Some supporters went on to the playing surface just before half-time when Esperance scored their first goal but they were quickly removed by security officials.
Tunisian football has largely been played behind closed doors since the revolution in the country last year, mainly due to fear of crowd violence.
A go-ahead for spectators to be allowed back to the grounds was recently granted at the behest of the financially-strained clubs.
Since the pitch invasion in Sousse, Tunisia's sports ministry has again banned fans until the end of the season next month.
Etoile's results from their four Group A games have been expunged, ensuring Esperance and Nigerians Sunshine Stars advance to the semi-finals in October.
Tunisians Etoile won the Champions League in 2007 but now face a two-year ban from CAF competition.