The Olympic Eagles returned from behind to grab maximum points and raise their tally to three points, leading Cote d’Ivoire on goal difference, and one shy of group leaders South Africa.
Zambia follow in order with a lone point before the final round of group games on Friday.
Patson Daka gave Zambia the lead after 12 minutes, ending a brilliant solo effort sending the ball past Adamu Abubakar to give Chipolopolo advantage.
But Zambia’s joy was short-lived when Orji Okwonkwo restored parity just four minutes later, tapping the ball from close range following a corner.
The first half ended with sides tied at 1-1.
Nigeria skipper Kelechi Nwakali took the lead for The Olympic Eagles sending a beautiful free-kick that wronged Zambia’s goalkeeper Mangani Banda after 65 minutes.
And deep into injury time, Taiwo Awonyi made use of a swift counter attack to add Nigeria’s third of the night.
Leaders South Africa face Nigeria at Al Salam Stadium, while Zambia takes on Cote d’Ivoire in a simultaneous kick-off on Friday at Cairo Stadium.