Five of the last six host nations to reach the final had been crowned AFCON champions, but the Ivory Coast's appearance in this edition at one point looked unlikely, their 4-0 group-stage defeat to Equatorial Guinea leading to the mid-tournament sacking of Jean-Louis Gasset.
The Elephants, who under caretaker boss Emerse Fae earned the nickname 'the Zombies' after resurrecting their campaign, recovered to reach the final but fell behind in the showpiece when Nigeria captain William Troost-Ekong headed in a 38th-minute opener against the run of play.
However, that was cancelled out by Franck Kessie in the second half midway through the second half as the Ivory Coast drew level.
And, with less than 10 minutes remaining, Haller, who in July 2022 was diagnosed with testicular cancer and returned to action with Borussia Dortmund just over a year ago, found the finishing touch to send the 60,000-seat Alassane Ouattara Stadium into raptures.
Former West Ham striker Haller looked to fire his side into an early lead when he flicked Simon Adingra's cross wide of Stanley Nwabali's right post, and, while the Elephants did not make much of a handful of early set-pieces, the hosts controlled more of the opening action than their more cautious opponents.
Max Gradel, playing in his fifth AFCON, sent a bicycle kick from the Ivory Coast's third corner into the side-netting, and there were little in the way of chances for Nigeria by just after the 25-minute mark, when a brief scuffle ensued after Victor Osimhen insisted he had been unduly elbowed by Evan Ndicka.
Nigeria boss Jose Peseiro was booked for a subsequent protest before temperatures and tempers were cooled with a drinks break.
The Super Eagles, seeking a fourth AFCON title, took an unlikely lead not long after Adingra called Nwabali into action with a sharp effort, when at the other end the Elephants could only half-clear a corner and ex-Watford defender Troost-Ekong looped his header past Yahia Fofana.
There was a nervy moment for Nigeria just after the break, when Nwabali stuck a hand out to block Adingra's cross, but the clearance travelled only as far as Gradel, whose shot stung the legs of Calvin Bassey and allowed time for the Nigeria keeper to make the save.
Kessie was next to push for an equaliser, sending a diving header straight at Nwabali, moments before the Nigeria shot-stopper pushed Odilon Kossounou's effort around his post.
The home crowd erupted when the hosts levelled with the resulting corner, Nigeria gifting Kessie a free header which he obligingly directed downward and past Nwabali.
Haller sent an overhead kick wide of the left post, while there looked worrying news for Nigeria when star striker Osimhen seemed to be in pain, landing awkwardly after battling Seko Fofana for the ball.
Though he had not succeeded with his earlier acrobatic effort, Haller succeeded in the 81st minute, when he diverted in Adingra's fine cross with a raised toe, securing both the trophy and his own national-hero status.
The hosts survived seven minutes of added time, clinging on for the nervy but well-deserved victory.
