The Red Devils needed a last-gasp header from defender Wael Gomaa to overcome their bitter rivals in the competition's group stage at Cairo Stadium.
The victory put Ahli in second place in Group B with four points, two behind JS Kabylie of Algeria after two matches. Nigeria's Heartland are third on one point.
Ismaili, who failed to bag any points, lie at the bottom after slumping to a 1-0 home defeat by Kabylie before suffering a heartbreaking loss to Ahli.
"Our victory tonight is very important, especially after Kabylie beat Heartland on Saturday," coach Hossam Al-Badri, who steered Ahli to Egyptian Super Cup triumph at the expense of Harras Hodoud last week, said after the game.
"There is a long way to go but we took a big step towards the semis.
"Ismaili still have hope of progressing to the next round but their task will be very difficult."
Striker Mohamed Talaat gave Ahli the lead in the 58th minute but Ismaili substitute Mohsen Abou-Greisha looked to have secured a share of spoils with a simple finish ten minutes from time.
Combative centre back Gomaa, who set up Talaat for the opener, notched the decisive goal four minutes into the stoppage time with a far-post header after a recurring lapse of concentration from Ismaili's defense.
"It's our habit, we go after the win at any time even in the dying seconds," Gomaa, who has recently extended his contract with the six-time African champions, said.
"We want to finish on top of the group."
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