The hosts controlled the early stages and opened the scoring in the 28th minute through Mahmoud Saber, who calmly slotted home a cross from the right.
Eric Chelle’s men responded strongly with centre-back Chidozie Awaziem equalising in first-half stoppage time, heading in Zaidu Sanusi’s well-delivered free kick from close range.
Both coaches made a few changes after the break, but it was the Pharaohs who found the decisive goal.
Mostafa Mohammed struck seven minutes into the second half to hand the hosts the victory.
Despite the defeat, the Super Eagles will now focus on their opening AFCON 2025 clash against the Taifa Stars of Tanzania next Tuesday.
Nigeria will travel to Fez, Morocco, on Thursday to begin preparations for the tournament, aiming to hit the ground running in their quest for a fourth continental title.