Ex- African Footballer of the Year the Napoli star helped his team build a 3-0 lead, before they were forced to hold on for a hard-fought win.
The three-time champions survived a stunning comeback attempt from their opponents to progress 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 clash in Fes, enjoying a 3-0 cushion with only 17 minutes remaining courtesy of goals from their attacking trio.
Yet, a Tunisian defender reduced the deficit with a close-range finish from a Hannibal Mejbri set-piece, sparking hopes of a turnaround.
The drama escalated when Tunisia were given a late penalty after a VAR review spotted a handling offense by the Nigerian defender. Ali Abdi calmly slotted home in the dying stages to create a nail-biting conclusion.
Tunisia came agonizingly close from a last-gasp leveler in stoppage time, with captain Ferjani Sassi directing a opportunity just past the post before Ismael Gharbi sent a half-volley past the upright.
This result means that Nigeria, champions of the competition on three past instances, move to six group points and are assured top spot in their pool with a match still to be contested.
In the next round, they will face a best third-place team from one of the other preliminary groups.
Meanwhile, Tunisia stay on three group points, with Uganda and Tanzania locked on a single point after registering a one-all stalemate in the day's other fixture.
The final group fixtures will see the group leaders remain in the city to play Uganda on Tuesday, while the Eagles of Carthage return to Rabat to confront the Taifa Stars.
The Tunisian defender drilled the ball from 12 yards to offer Tunisia hope of snatching a draw.
Nigeria, finalists in the previous tournament, are the next nation after the Pharaohs to qualify for the next phase, but coach Eric Chelle and fans will undoubtedly be breathing a sigh of relief.
What looked like set to be a comfortable final quarter transformed into a nerve-wracking affair.
The prolific striker had a goal disallowed for an infringement before opening the scoring on the stroke of half-time, expertly guiding a glancing effort into the bottom corner from an Atalanta winger cross.
The advantage was extended soon in the second half when Wilfred Ndidi climbed above everyone to power home a header from a set-piece kick.
The number 9 then turned provider Lookman for the seemingly decisive goal, only for the defender to direct a header past the Nigerian shot-stopper to begin the comeback.
The pivotal incident arrived when a high ball hit the arm of Bright Osayi-Samuel, with the official pointing to the spot after consulting the VAR monitor.
Although the defender's successful penalty, the 2004 champions ultimately came up just short of completing a remarkable comeback.
Their fate is still in their control; 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 led to his previous resignation.
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