Ex- African Footballer of the Year Victor Osimhen was instrumental in his team establish a 3-0 advantage, but they were compelled to hold on for a narrow victory.
The three-time champions survived a dramatic comeback attempt from Tunisia to advance to the last 16 of the 2025 Africa Cup of Nations being held in the host nation.
Jose Peseiro's side seemed to be in complete control in their pool clash in Fes, enjoying a three-goal cushion with just 17 minutes left courtesy of goals from their attacking trio.
Yet, a Tunisian defender pulled one back with a close-range finish from a Hannibal Mejbri set-piece, igniting hopes of a turnaround.
The tension escalated when the North Africans were given a spot-kick after a video assistant referee check identified a handling offense by the Nigerian defender. Ali Abdi converted in the 87th minute to create a frantic conclusion.
Tunisia came agonizingly close from a last-gasp equalizer in added time, with their skipper directing a opportunity narrowly wide before a substitute guided a bobbling volley past the goal frame.
This result means that the Super Eagles, winners of the competition on 3 past instances, move to six group points and are guaranteed top spot in their pool with one game left to be contested.
In the next round, they will meet a third-placed side from either the other preliminary groups.
In the other match, Tunisia stay on 3 group points, with the East African teams tied on one point each after playing out a 1-1 draw in the day's other fixture.
The concluding pool matches will see Nigeria stay in Fes to play the Cranes on Tuesday, while Tunisia travel back to the capital to face Tanzania.
The Tunisian defender smashed the ball from the penalty spot to offer his team a glimmer of hope of earning a point.
The Super Eagles, finalists in the previous tournament, become the second nation after the Pharaohs to qualify for the knockout stage, but their manager and supporters will undoubtedly be feeling relieved.
What seemed set to be a comfortable final quarter morphed into a tense conclusion.
Victor Osimhen had a effort ruled out for an infringement before breaking the deadlock right before half-time, expertly guiding a glancing effort into the far post from an Ademola Lookman delivery.
The advantage was extended soon in the second half when the Leicester City midfielder rose highest to thump in a header from a Lookman kick.
Osimhen then turned provider his teammate for the seemingly decisive goal, only for Montassar Talbi to steer a header past the Nigerian shot-stopper to begin the fightback.
The key moment arrived when a high ball hit the arm of Bright Osayi-Samuel, with referee Boubou Traore pointing to the spot after consulting the VAR monitor.
Although the defender's successful penalty, the 2004 champions ultimately fell short of completing a stirring recovery.
Tunisia's destiny remains in their own hands; a draw against Tunisia will be sufficient to see them through, and manager Sami Trabelsi will be keen to avoid a recurrence of the past group-stage exit that resulted in his previous resignation.
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