Afouane Gharbi stunned the home crowd just before the break but Emad Al-Nahhas grabbed the equalizer shortly after the interval.
However, Al-Nahhas was sent-off for a reckless challenge to leave Ahli with a mountain to climb.
Two goals in stoppage time from Amine Chermiti and Moussa Nary gave Etoile their first ever Champions League title.
Ahli were looking to claim a third successive African title and a record-breaking sixth triumph, but their hopes were dashed by the Tunisians.
The Cairo giants played a good first-half and laid siege to the Tunisian areas but couldn't break the deadlock.
Emad Meteb was denied by the crossbar in the 20th minute and Mohamed Abou-Treika's shot passed the goal line but the goal was ruled for offside.
Angola's Gilberto crossed more than once and compatriot Flavio was pain in Etoile's side.
Shocking opener
However, it was Etoile who went ahead against the run of play.
Gharbi's volley from Saber Ben Frej's cross took deflection from Ahli captain Shadi Mohamed and floated past Essam Al-Hadari.
Shadi tried to block the shot but he converted the ball into his own net.
Al-Nahhas drew Ahli level five minutes after re-start when he rose unmarked to head Gilberto's pinpoint free-kick past Etoile keeper Aymen Mathlouthi, who got a hand to the ball.
Ahli then launched wave of attacks as they their enthusiasm was fuelled by the fans' huge support.
Abou-Treika should have put the hosts in front in the 52nd minute when he controlled a low pass inside the area before turning and firing a low shot just wide of the post.
Two minutes later, Flavio's overhead kick narrowly missed the target before the Angolan striker was involved in a scuffle with an opponent.
Abou-Treika, who was kept at bay most of the game, appealed for penalty in the 57th minute when he was brought down by Radhouene Felhi.
Television replays showed that Felhi made a stiff tackle against the classy playmaker.
Turning point
Al-Nahhas was made to pay for his sluggishness after he was handed a straight red card.
Chermiti got the better of Al-Nahhas and went clear on goal, leaving the former Egyptian international with no alternative but to haul him down.
The red card proved to be a turning point in the game as Etoile capitalized on the gaps in Ahli defense to make dangerous counter attacks.
Etoile could have taken advantage of their numerical advantage two minutes past the hour mark when Gharbi's curling free-kick cannoned off the crossbar.
Al-Hadari brilliantly blocked a powerful shot one minute into additional time, but he couldn't help shortly after.
After several wasted attempts to kill off the game, Chermiti put the result beyond doubt when he went on-one-one and coolly slotted the ball past the advancing Al-Hadari.
Narry completed the rout just before the final whistle with a low bullet from the edge of the area.