The hosts were good value for their 1-0 lead, with Oghenekaro Etebo on target in the 59th minute at a packed Ahmadu Bello Stadium in Kaduna.
If not for an impressive performance in goal by Ahmed El-Shennawi and some wayward finishing from Odion Ighalo, Samson Siasia would have been celebrating a handsome start to his second stint as Nigeria coach.
But Etebo went from hero to villain as he played Salah onside in stoppage time and the Roma winger made no mistake.
Siasia handed a maiden international start to Manchester City forward Kelechi Iheanacho and his attacking line-up began on the front foot.
But Egypt almost broke the deadlock in the 18th minute as Mohamed Salah and Abdallah El-Said combined for Koka to draw a superb save from Carl Ikeme.
El-Shennawi got down got down sharply at the other end to deny Moses Simon and kept out an Iheanacho drive as half-time approached before Watford striker Ighalo spurned a close-range opportunity.
Egypt’s resistance was broken shortly before the hour when Iheanacho’s snapshot struck the bar and fell for Etebo to smuggle home at the back post.
Nigeria pushed for a second and El-Shennawi made further excellent stops from Ighalo and substitute Victor Moses.
Moses rounded the keeper in the 84th minute, only for Rami Rabia to clear off the line and that intervention would prove crucial when Salah punished Siasia’s men in stoppage time, maintaining Egypt’s advantage ahead of Tuesday’s return clash.