Pyramids FC celebrate their late win over Sfaxien
Gabr met an inviting corner from veteran playmaker Abdallah El-Saed with a well-placed header at the far post in stoppage time.
Pyramids are on top of Group A with maximum nine points, six ahead of second-placed Club Sfaxien.
Libya's Ahli Tripoli, who lie third with three points, host Zambia's Zanaco in the other group match later on Sunday.
Pyramids were unconvincing throughout and were almost punished in the dying minutes when Firas Chawat's acrobatic effort missed the target.
Forward Ibrahim Adel had the chance to put Pyramids ahead in the 20th minute when El-Said released him but his close-range effort was denied by the keeper.
Ten minutes later, El-Said squandered a golden chance when his shot was deflected by a Sfaxien defender with the goal at his mercy.
Pyramids remained in control in terms of possession in the second half but could not make the most of the few chances they created.
New-signing Fagrie Lakay, who scored twice in the previous game against Ahli Tripoli, was also guilty of a miss when El-Said played him in.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)