Ahly remain top of the table with 55 points, two ahead of second-placed Pyramids FC, who defeated Petrojet 2-0 also on Saturday.
Midfielder Emam Ashour opened the scoring in the 21st minute with a powerful strike from outside the area, moving him to the top of the league's scoring chart with 12 goals.
Togolese striker Yaw Annor levelled for NBE Club just before halftime, dribbling past defenders in the box before calmly slotting home.
Abou Ali, who came on at the start of the second half in place of Nejc Gradisar, netted the decisive goal in the sixth minute of added time, converting from close range after a well-placed assist by defender Yasser Ibrahim.
Ahly coach Emad El-Nahhas also introduced Amr El-Sulaya, Mohamed “Afsha” Magdi and Hussein El-Shahat in the second half to revitalise his side.
El-Sulaya came close with a powerful long-range effort that forced a save from NBE goalkeeper Abdel Aziz El Balouti.
Both teams had limited chances in the second half, with possession evenly shared, but Ahly’s late push proved enough to secure the three points.
Ahly will face Pharco FC on Wednesday, 28 May, in the final round of the Playoff stage, where they could celebrate the league title.
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