Nigeria seized an early lead through a first-time volley from outside the area by Paul Onuachu in the opening minute.
The Nigerians closed in on a second, but Alex Iwobi failed to profit from a poor defensive clearance with a tame effort on the half-hour mark.
With the visitors proving little of a threat, the West Africans went to the halftime interval in control of proceedings.
In the second half, Nigeria gave a run to reserve goalkeeper Ikechukwu Ezenwa for Daniel Akpeyi right from the restart.
The Egyptians still battled to trouble the Nigerians, who threatened a second goal through Onuachu’s header from a free-kick on 58 minutes.
With just under 20 minuets to go, Iwobi played a one-two with Henry Onyekuru near the edge of the area but after getting goal-side, failed to beat Mahmoud Abdel Rahim.
The Super Eagles were given their first real scare of the game with seven minutes remaining, but Ezenwa produced a good save to palm Amr Warda’s shot into touch.
In the end, the Super Eagles walked away victors by a narrow margin, as the Pharoahs head back to the drawing board.