"We expected to win but not this way," Etoile's Hatem Bejaoui said.
"3-1 is a heavy defeat for Al-Ahly."
Etoile took the lead in first-half stoppage time through Afouene Gharbi only for defender Emad al-Nahas to equalise five minutes into the second half of a thrilling climax watched by a capacity crowd of 50,000.
Needing to score again under the away-goal rule, Ahly laid siege to the Etoile goal until veteran Nahas was shown a red card by Moroccan referee Abderrahim al-Arjoun.
Ahly never regained their momentum with 10 men and survived a few scares before Amine Chermiti put Etoile 2-1 ahead two minutes into stoppage time and Mohamed Ali Nafkha added a late third goal to make sure of victory.
Lifting the trophy completed a clean sweep of CAF titles for Etoile who have won the Cup Winners Cup and CAF Cup twice and the Super Cup and Confederation Cup once.
Crowd trouble after the match
Al-Ahly fans throw wooden chairs at Etoile
players after the trophy ceremony [AFP]
Egyptian security forces were deployed around the stadium in expectation of trouble between the rival fans, but tensions inside the stadium boiled over as the trophy was handed to the Tunisians, with police intervening after Egyptian fans started grabbing Etoile players.
Police took players from both sides and Manuel Jose, Al-Ahly coach, inside after fans began spitting on the losers.
Etoile, twice Champions League runners-up, became more assertive as the opening half drew to a close and they silenced a largely Egyptian crowd by taking the lead one minute into stoppage time.
Muri Ogunbiyi passed to stand-in captain Saber Ben Frej on the right wing and his cross found unmarked Gharbi, whose shot was deflected past goalkeeper Essam al-Hadary into the corner of the net.
Coach Jose swapped Ahly midfielders at half-time, replacing Islam al-Shatar with Hassan Mostafa, and five minutes into the second half they were level when Nahas headed home a Felisberto 'Gilberto' Amaral free kick.
The hero turned villain 11 minutes later when he fouled Chermiti and Arjoun, giving one of the finest performances by a referee in an African club match, did not hesitate to expel Nahas.
Gharbi hit the crossbar from a free kick, Gilson 'Ja' Silva fired wide when well-placed and Hadary saved superbly from Bassem Ben Nasr before Etoile struck twice late to take the trophy back to Tunisia after a 131-year absence.