Former African Footballer of the Year the Napoli star was instrumental in his team build a commanding advantage, but the Super Eagles were forced to defend resolutely for a hard-fought victory.
Nigeria weathered a dramatic late rally from Tunisia to progress to the last 16 of the Afcon tournament taking place in Morocco.
The Super Eagles seemed to be in complete control in their Group C encounter in the Moroccan city, holding a three-goal cushion with just a quarter of an hour left courtesy of goals from Victor Osimhen, Wilfred Ndidi and Ademola Lookman.
However, a Tunisian defender pulled one back with a powerful header from a Manchester United midfielder set-piece, igniting hopes of a turnaround.
The drama escalated when Tunisia were given a spot-kick after a video assistant referee review spotted a handling offense by Bright Osayi-Samuel. The left-back calmly slotted home in the dying stages to set up a frantic conclusion.
The Carthage Eagles came agonizingly close from a last-gasp equalizer in added time, with their skipper directing a chance just past the post before a substitute guided a bobbling volley wide of the upright.
The victory ensures that the Super Eagles, champions of the competition on three previous occasions, move to 6 group points and are assured top spot in their pool with a match still to be contested.
In the next round, they will meet a best third-place side from one of Group A, B or F.
In the other match, Tunisia remain on three points, with Uganda and Tanzania tied on one point each after playing out a 1-1 stalemate in the day's other fixture.
The concluding group fixtures will see the group leaders remain in the city to play the Cranes on the next matchday, while Tunisia travel back to Rabat to confront Tanzania.
The Tunisian defender smashed the ball from 12 yards to offer Tunisia a glimmer of hope of earning a draw.
The Super Eagles, finalists in the 2023 tournament, become the second team after the Pharaohs to reach the knockout stage, but coach Eric Chelle and supporters will certainly be feeling relieved.
What looked like set to be a comfortable last period transformed into a tense affair.
Victor Osimhen had a effort disallowed for an infringement before breaking the deadlock right before the interval, expertly guiding a glancing effort into the far post from an Atalanta winger cross.
The lead was doubled early in the second half when Wilfred Ndidi climbed above everyone to thump in a powerful nod from a set-piece kick.
The number 9 then set up his teammate for the seemingly decisive goal, before Montassar Talbi to direct a powerful header past goalkeeper Stanley Nwabali to begin the comeback.
The key incident arrived when a high ball struck the arm of the full-back, with the official pointing to the spot after reviewing the VAR monitor.
Despite Ali Abdi's confident conversion, Tunisia ultimately fell short of pulling off a stirring comeback.
Tunisia's destiny remains in their own hands; a draw against Tunisia will be enough to secure progression, and manager Sami Trabelsi will be keen to prevent a repeat of the past early elimination that led to his departure.
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