The Angolan opened the scoring two minutes after the restart through a near-post header after being set-up by his compatriot Gilberto.
Ivorian striker Kouassi Blaise equalized three minutes past the hour mark but Flavio once again came to Ahli's rescue.
Gilberto was again the provider to help the Petro Atletico man power a super header into the net 20 minutes from time.
The victory helped Ahli surpass arch-rivals Zamalek, who won the annual one-match competition three times.
Abou-Treika Missed
Ahli sorely missed the presence of influential playmaker Mohamed Abou-Treika, who was ruled out of the game due to a niggling knee injury.
Veteran midfielders Ahmed Hassan and Mohamed Barakat, who were given advanced roles, failed to assist lone striker Flavio.
Sfaxien's steadfast defense restricted Ahli to some tame efforts in the first half.
The Red Devils had one golden opportunity to break the deadlock after 18 minutes but were denied by a superb save from Sfaxien keeper Jassem Khaloufi.
Gilberto's long-range free-kick found the unmarked Hassan, whose free header was blocked by Khaloufi from point-blank range.
Sfaxien also squandered a clear-cut opportunity to stun the home crowd after capitalizing on some sloppy defending from Ahli's sluggish backline.
Seven minutes before the break, a low cross from the right picked out Sfaxien playmaker Abdel Karim Nafti, whose deft back-heeled pass found striker Hamza Younes.
The unmarked Younes could only roll a weak shot that looked to be on its way into the net although keeper Amir Abdul-Hamid got a hand to it.
A last-minute interception by versatile midfielder Ahmed Fathi prevented Sfaxien from having the lead.
Unstoppable
The unstoppable Flavio made the difference in the second period.
He gave Ahli the lead in the 47th minute when he beat his marker to Gilberto's right-wing corner to head past Khaloufi.
But the Cairo giants' shaky defense cost them in the 63rd minute as Sfaxien restored parity.
In the 63rd minute, Younes darted down the right flank before providing a low cross to the onrushing Blaise, who ghosted behind Ahmed Fathi to slot in at the far post.
Flavio came close to restoring Ahli's advantage six minutes later when he met a Fathi cross with a glancing header that narrowly missed the target.
He made amends shortly after to score the winner as he connected with another pinpoint cross from Gilberto to send an exquisitely-directed header into the back of the net.
Watch some highlights and Ahli's post-match celebrations