William Troost-Ekong's second-half penalty was enough to earn the Super Eagles' first win of the campaign, which puts them alongside Equatorial Guinea at the top of the group before the final round of games.
Lively starts have become par for the course at this AFCON and both teams looked to strike early, Victor Osimhen firing over from a excellent ball in behind before Christian Kouame was unable to take advantage of a Nigeria error at the other end.
Evan Ndicka shot tamely straight at Super Eagles goalkeeper Stanley Nwabali on the quarter-hour mark but Ivory Coast struggled to break down the solid defence of Nigeria's 5-4-1 formation off the ball.
While Jose Peseiro's gameplan of sitting deep and breaking with pace looked promising in flashes, it led to a tight, scrappy affair until the opening goal arrived after the break.
Osimhen was caught late by Ousmane Diomande in the Ivorians' area which prompted a VAR review and the award of a spot-kick. Captain William Troost-Ekong stepped up to slam home from 18 yards.
The hosts are behind! 😲
William Troost-Ekong was not messing around with that penalty! 💥 pic.twitter.com/sK2eIIp0pu
— Sky Sports Football (@SkyFootball) January 18, 2024
Les Elephants were prompted into a triple change as ex-Arsenal winger Nicolas Pepe arrived on the scene to spark their attack, and an increasingly frustrated home crowd, into life.
Seko Fofana and Ndicka saw late attempts flash off-target but Nwabali went untested as Nigeria secured a vital three points, effectively sealing their route into the last-16 as at least a best third-placed side ahead of meeting Guinea-Bissau.
Ivory Coast are due back at the Stade Alassane Ouattara on Monday for a showdown with Equatorial Guinea, when a defeat could see the hosts knocked out.