The Elephants were one of three contenders battling for a top-two berth in Group F, ahead of facing a Gabon side whose AFCON journey was already over.
The Panthers may have been expected to exit the tournament quietly, but Thierry Mouyouma’s side clearly didn’t get the memo after racing into a 2-0 lead inside 21 minutes.
Guelor Kanga reacted first on the rebound after Alban Lafont failed to deal with Teddy Averlant’s shot to break the deadlock, before Denis Bouanga doubled their advantage with a wonderful first-time strike into the bottom corner.
Emerse Fae’s side were rattled, but came within inches of halving the deficit when Oumar Diakite’s ferocious effort cannoned off the woodwork following some neat link-up play with Franck Kessie.
The Elephants did pull one back before half-time, though, as Wilfried Zaha laid the ball on a plate for Jean-Philippe Krasso to tap home from point-blank range.
With some improved finishing, Gabon may not have been heading on an early flight home. They spurned two golden opportunities to add a third after the restart when Clench Loufilou somehow fired wide at the far post, before Averlant failed to find the target with his own close-range strike.
Fae introduced Manchester United starlet Amad Diallo from the bench to boost their comeback bid, but his first action was to fire a free-kick harmlessly over the bar.
Another substitute would go on to level the scores, as Christopher Operi delivered an enticing corner for Evann Guessand to meet with a brilliant towering header, seemingly sealing a point for the reigning champions.
There was still time for the Elephants to steal this game at the death, as Bazoumana Toure’s brilliant diving header from Operi’s cross moved them in front and sealed all three points, before Yan Diomande had a fourth ruled out for offside.
This win seals top spot in the group, ahead of a Cameroon side that overcame Mozambique 2-1 in tonight’s other late game. Although with Mozambique also progressing - as one of the best third-placed sides - Gabon will feel in isolated company, despite already knowing their fate.
Flashscore Man of the Match: Christopher Operi (Ivory Coast)