The former Ghazl Mahalla striker, who came on as a second-half substitute, broke the deadlock seven minutes after the restart to notch his first goal for Ahli.
Veteran midfielder Ahmed Hassan doubled the advantage two minutes past the hour mark.
Right-back Ahmed Sedik wrapped up the victory five minutes from time after being set-up by Farag.
The Red Devils, who won the cup 35 times, will face Harras Al-Hodoud in the next round after the latter defeated Abou Qurqas Sugar 4-1.
Winning Ways
Ahli were eager to make up for their disappointing sixth-place finish in the FIFA Club World Cup earlier this month.
They managed to return to winning ways at the expense of Alexandria-based club Koroum.
Ahli coach Manuel Jose fielded a second-string line-up to keep his regular players fresh ahead of a hectic schedule.
Midfielder Hussein Ali and Palestinian keeper Ramzi Saleh made their competitive debuts while playmaker Mahmoud Samir was given a rare starting berth.
The first-half was a dull affair, with neither side being able to create clear-cut opportunities.
Ahli's only chance came five minutes before the break when Koroum keeper tipped Samir's shot onto the bar.
Farag put the Cairo giants in front in the 52nd minute with a precise shot from inside the area after a goal-mouth scramble.
The 26-year-old's goal might convince Jose to keep hold of him as numerous reports suggested that his days at Ahli were numbered.
Hassan, who was also introduced in the second half, extended Ahli's lead in the 62nd minute after firing a powerful long-range drive that left the keeper with no chance.
Sedik ensured the win in the 85th minute when he was found unmarked by Farag's cross to send a first-timer into the near top corner.