Ayman Ashraf, Karim Fouad, Aliou Dieng and Ahmed Abdel Kader were restored to Ahly’s line-up, while South Africa’s Percy Tau also started following a return from injury.
The holders looked to settle first following the first 20 minutes from a flowing move involving Tau, Mohamed Sherif as well as Mohamed Magdy Afsha.
Ahly enjoyed the lion's share of play in the opening exchanges, but the high-defensive line approach the visitors made life difficult for Tau and co.
That allowed Hilal the opportunity to come alive well inside the half-hour mark and question Ahly from a free-kick by former Baroka FC man Gerald Phiri Junior.
An injury forced the Sudanese giants to introduce a substitution four minutes before halftime, with David Uromi brought in for Yasir Mozami Mohamed El Tayeb.
Pitso Mosimane’s side struggled to settle in the second half before a one-two around the area presented Tau an opportunity from a tight angle, but he failed to profit.
Another promising moment after a few minutes fell to Ahly when a glancing header in the box from Kader flashed across the face of goal with Hussein El Shahat introduced for Sherif.
The change was just what the defending champions needed as El Shahat found an open space in the area to side-foot home from good work by Kader inside the final ten minutes.
El Shahat could’ve registered a brace in the last seven minutes from a loose ball involving Tau outside the area, but the attacker curled beyond the top corner.
Hilal pushed for a late turnaround, but the holders managed to see out the closing stages for the win and a spot in the knockout stages.