Mohamed Salah was silenced in a shocker from the Pharoahs, and Nigeria top Group D.
The match began cagily for both sides, with neither keeper tested early on.
Liverpool’s Mohamed Salah, who was often isolated in the first half, dropped deeper to attempt to influence the play but failed to challenge the Super Eagles backline in the opening period.
Moses Simon’s mazy run produced the game’s first chance, beating three Egypt defenders before blasting into Mohamed El Shanawy’s side netting.
Pressure mounted, and finally wilted for Egypt when Kelechi Iheanacho found the top corner.
Simon’s cross was poorly cleared by Ahmed Hegazy, allowing Joe Aribo to find the Leicester City striker on the edge of the box. His half-volley was unstoppable, sending Nigeria fans into raptures.
It was his first international goal since September, when he struck twice in a two-nil win over Liberia in World Cup qualifying.
In the second half, the same themes continued, with Nigeria capitalising on Egypt defensive frailties. They very nearly made it two when Mahmoud Hamdy’s tackle fell into the path of Iheanacho. Luckily for Carlos Queiroz’s side, he scuffed his touch.
Egypt began to look more encouraged as the half went on, but they failed to test Watford’s new signing Maduka Okoye in the Super Eagles net until Mohamed Salah scrambled an effort into his midriff.
Nigeria then suffered a setback with Kenneth Omeruo, stricken by an injury, was replaced by Semi Ajayi. The former Chelsea defender fell awkwardly after a corner, and could be a big miss for Augustine Eguavoen.
A late wave of Egypt pressure nearly resulted in another Nigeria goal, but a fine stop from El-Shanawy denied substitute Chidera Ejuke.
Nigeria deservedly won, and top Group D. Sudan and Guinea-Buissau face off later on in the remaining fixture.
Nigeria: Okoye; Aina, Troost-Ekong, Omeruo, Sanusi; Aribo, Ndidi, Simon; Chukwueze, Awoniyi, Iheanacho
Egypt: El Shenawy; Hegazy, Hamdy, Fathi; Tawfik, Trezeguet, Elneny, Fattoh; Marmoush, Mohamed; Salah
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