Former African Footballer of the Year the Napoli star was instrumental in Nigeria establish a 3-0 advantage, but they were compelled to hold on for a narrow victory.
The three-time champions survived a stunning comeback attempt from Tunisia to advance to the knockout stage of the Afcon tournament being held in the host nation.
Jose Peseiro's side seemed to be in complete control in their Group C encounter in Fes, holding a three-goal cushion with only 17 minutes left thanks to strikes from Victor Osimhen, Wilfred Ndidi and Ademola Lookman.
Yet, Montassar Talbi pulled one back with a close-range finish from a Manchester United midfielder set-piece, igniting hopes of a recovery.
The drama escalated when Tunisia were given a spot-kick after a video assistant referee review identified a handling offense by the Nigerian defender. The left-back calmly slotted home in the 87th minute to set up a frantic conclusion.
The Carthage Eagles came agonizingly close from a stunning leveler in stoppage time, with their skipper heading a chance just past the post before a substitute sent a bobbling volley wide of the goal frame.
The victory means that the Super Eagles, champions of the tournament on 3 previous occasions, advance to 6 group points and are assured top spot in Group C with one game still to play.
For the round of 16, they will meet a best third-place side from one of the other preliminary groups.
In the other match, the 2004 champions remain on 3 points, with Uganda and Tanzania tied on one point each after playing out a 1-1 draw earlier on Saturday.
The concluding pool matches will see Nigeria remain in the city to take on the Cranes on the next matchday, while the Eagles of Carthage return to the capital to face Tanzania.
Ali Abdi drilled home from the penalty spot to offer Tunisia a glimmer of hope of earning a point.
Nigeria, runners-up in the previous edition, become the second nation after Egypt to reach the next phase, but coach Eric Chelle and fans will undoubtedly be breathing a sigh of relief.
What seemed set to be a comfortable final quarter transformed into a nerve-wracking affair.
The prolific striker had a effort ruled out for an infringement before opening the scoring on the stroke of half-time, expertly guiding a header into the bottom corner from an Atalanta winger cross.
The advantage was doubled early in the second half when the Leicester City midfielder climbed above everyone to thump in a powerful nod from a Lookman kick.
Osimhen then turned provider his teammate for the seemingly decisive goal, before the defender to steer a header past the Nigerian shot-stopper to begin the comeback.
The pivotal incident came when a looping cross hit the forearm of Bright Osayi-Samuel, with the official pointing to the spot after consulting the pitchside screen.
Despite Ali Abdi's successful penalty, Tunisia in the end fell short of pulling off a stirring comeback.
Tunisia's destiny remains in their control; a draw against Tanzania will be enough to see them through, and manager Sami Trabelsi will be keen to avoid a recurrence of the 2013 early elimination that led to his previous resignation.
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