Former Continent's Best Player of the Year Victor Osimhen was instrumental in his team build a 3-0 advantage, but they were forced to hold on for a hard-fought win.
The three-time champions weathered a stunning comeback attempt from Tunisia to advance to the knockout stage of the 2025 Africa Cup of Nations being held in the host nation.
The Super Eagles appeared to be cruising in their Group C encounter in the Moroccan city, holding a three-goal cushion with just 17 minutes remaining courtesy of strikes from Victor Osimhen, Wilfred Ndidi and Ademola Lookman.
Yet, a Tunisian defender pulled one back with a close-range finish from a Manchester United midfielder free-kick, igniting hopes of a turnaround.
The tension escalated when Tunisia were awarded a spot-kick after a VAR check identified a handball by the Nigerian defender. Ali Abdi converted in the 87th minute to set up a frantic finale.
Tunisia came agonizingly close from a last-gasp equalizer in stoppage time, with their skipper directing a opportunity narrowly wide before a substitute sent a half-volley past the upright.
The victory ensures that the Super Eagles, winners of the tournament on 3 past instances, move to six group points and are guaranteed first place in their pool with a match left to be contested.
For the round of 16, they will face a best third-place team from one of the other preliminary groups.
In the other match, Tunisia remain on three points, with Uganda and Tanzania tied on one point each after playing out a one-all draw earlier on Saturday.
The concluding group matches will see Nigeria remain in Fes to take on the Cranes on Tuesday, while Tunisia travel back to Rabat to confront the Taifa Stars.
The Tunisian defender drilled home from 12 yards to offer his team a glimmer of hope of snatching a draw.
The Super Eagles, finalists in the previous edition, become the second nation after Egypt to reach the next phase, but coach Eric Chelle and supporters will undoubtedly be breathing a sigh of relief.
What looked like set to be a comfortable last period morphed into a nerve-wracking affair.
The prolific striker had a effort ruled out for offside before opening the scoring on the stroke of half-time, expertly guiding a header into the bottom corner from an Ademola Lookman delivery.
The advantage was doubled early in the second half when Wilfred Ndidi climbed above everyone to power home a header from a Lookman kick.
The number 9 then set up Lookman for the third goal, only for Montassar Talbi to steer a header past the Nigerian shot-stopper to initiate the comeback.
The key moment arrived when a looping cross hit the arm of the full-back, with the official awarding a penalty after reviewing the VAR monitor.
Although the defender's confident conversion, the 2004 champions ultimately fell short of completing a stirring comeback.
Tunisia's destiny is still in their own hands; a draw against Tunisia will be enough to see them through, and their coach will be eager to prevent a recurrence of the past early elimination that resulted in his previous resignation.
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