Former African Footballer of the Year Victor Osimhen was instrumental in his team build a 3-0 advantage, but the Super Eagles were forced to defend resolutely for a narrow victory.
The three-time champions survived a stunning late rally from their opponents to advance to the knockout stage of the 2025 Africa Cup of Nations taking place in the host nation.
Jose Peseiro's side seemed to be in complete control in their Group C clash in the Moroccan city, holding a three-goal cushion with just 17 minutes left courtesy of goals from Victor Osimhen, Wilfred Ndidi and Ademola Lookman.
Yet, a Tunisian defender reduced the deficit with a powerful header from a Manchester United midfielder free-kick, sparking hopes of a turnaround.
The drama escalated when the North Africans were awarded a late penalty after a VAR check identified a handling offense by the Nigerian defender. Ali Abdi calmly slotted home in the 87th minute to set up a frantic finale.
Tunisia were inches away from a last-gasp leveler in added time, with their skipper heading a opportunity narrowly wide before a substitute sent a half-volley past the upright.
The victory ensures that the Super Eagles, champions of the competition on three past instances, move to six group points and are assured top spot in Group C with one game left to be contested.
In the next round, they will meet a best third-place side from one of Group A, B or F.
Meanwhile, Tunisia stay on 3 group points, with Uganda and Tanzania tied on a single point each after registering a 1-1 stalemate earlier on Saturday.
The final group fixtures will see the group leaders stay in the city to play the Cranes on the next matchday, while Tunisia return to the capital to confront Tanzania.
Ali Abdi smashed home from 12 yards to give Tunisia hope of snatching a draw.
Nigeria, runners-up in the 2023 edition, are the next nation after Egypt to qualify for the knockout stage, but their manager and fans will undoubtedly be breathing a sigh of relief.
What looked like set to be a straightforward last period transformed into a tense conclusion.
The prolific striker had a goal ruled out for an infringement before breaking the deadlock right before the interval, precisely placing a header into the bottom corner from an Atalanta winger delivery.
The advantage was doubled soon in the second period when the Leicester City midfielder climbed above everyone to thump in a powerful nod from a Lookman kick.
The number 9 then turned provider Lookman for the third goal, only for the defender to direct a powerful header past the Nigerian shot-stopper to initiate the comeback.
The pivotal moment arrived when a looping cross struck the arm of the full-back, with referee Boubou Traore pointing to the spot after consulting the VAR monitor.
Despite Ali Abdi's successful penalty, the 2004 champions in the end came up just short of pulling off a remarkable recovery.
Their fate is still in their own hands; a point against Tanzania will be sufficient to see them through, and their coach will be eager to avoid a recurrence of the past group-stage exit that resulted in his previous resignation.
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