Former Continent's Best Player of the Year the Napoli star helped his team build a commanding lead, before they were compelled to hold on for a narrow win.
The three-time champions survived a dramatic comeback attempt from their opponents to advance to the knockout stage of the Afcon tournament taking place in Morocco.
Jose Peseiro's side seemed to be in complete control in their Group C encounter in Fes, holding a three-goal lead with just a quarter of an hour left thanks to strikes from Victor Osimhen, Wilfred Ndidi and Ademola Lookman.
However, a Tunisian defender pulled one back with a close-range finish from a Hannibal Mejbri free-kick, igniting hopes of a turnaround.
The tension intensified when Tunisia were given a spot-kick after a VAR review spotted a handling offense by Bright Osayi-Samuel. Ali Abdi calmly slotted home in the dying stages to create a nail-biting conclusion.
The Carthage Eagles came agonizingly close from a stunning leveler in stoppage time, with their skipper directing a opportunity narrowly wide before Ismael Gharbi guided a bobbling volley wide of the goal frame.
This result ensures that the Super Eagles, champions of the competition on 3 previous occasions, advance to 6 points and are assured top spot in their pool with one game still to play.
In the next round, they will face a best third-place side from one of the other preliminary groups.
Meanwhile, Tunisia remain on three points, with the East African teams tied on one point after playing out a 1-1 stalemate in the day's other fixture.
The concluding group matches will see the group leaders remain in the city to take on the Cranes on Tuesday, while the Eagles of Carthage travel back to the capital to confront the Taifa Stars.
The Tunisian defender smashed the ball from the penalty spot to offer Tunisia a glimmer of hope of snatching a point.
Nigeria, finalists in the previous tournament, become the next nation after Egypt to reach the next phase, but their manager and fans will certainly be breathing a sigh of relief.
What looked like set to be a comfortable final quarter morphed into a tense conclusion.
The prolific striker had a goal ruled out for offside before breaking the deadlock on the stroke of the interval, precisely placing a header into the bottom corner from an Ademola Lookman cross.
The advantage was extended soon in the second half when Wilfred Ndidi rose highest to thump in a powerful nod from a Lookman corner.
Osimhen then set up Lookman for the third goal, before Montassar Talbi to direct a powerful header past the Nigerian shot-stopper to initiate the fightback.
The pivotal incident arrived when a looping cross struck the forearm of Bright Osayi-Samuel, with referee Boubou Traore pointing to the spot after consulting the pitchside screen.
Despite the defender's confident conversion, the 2004 champions ultimately came up just short of pulling off a stirring recovery.
Their fate is still in their control; a point against Tanzania will be sufficient to secure progression, and manager Sami Trabelsi will be keen to prevent a recurrence of the 2013 early elimination that resulted in his departure.
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