Ivory Coast dominated most of the first half in front of a fervent crowd at the Alassane Ouattara Stadium, but failed to carve out chances as Nigeria sat deep and soaked up pressure.
The game sparked into life after the drinks break on the half-hour mark, with Nigeria goalkeeper Stanley Nwabali blocking Adingra's shot from a narrow angle before Nigeria left-back Zaidu Sanusi won a corner when his effort was blocked by Odilon Kossounou.
Ademola Lookman's inswinging corner was headed up into the air by Ivory Coast midfielder Jean Michael Seri at the near post, and Troost-Ekong leapt above Serge Aurier to guide the ball back across goal and past the despairing dive of Elephants keeper Yahia Fofana.
The Ivorians came out with renewed purpose after the break, with the lively Adingra at the heart of their best moments on the left flank.
A dangerous low cross from the Brighton winger was tipped away by Nwabali and Calvin Bassey made a crucial block to prevent an equaliser after Max Gradel pounced on the loose ball.
Nwabali then had to dive to his right to scramble a long-range shot from Kossounou wide, and the Elephants equalised from the resulting corner as the Nigeria defence somehow failed to pick up Kessie.
The Super Eagles had a chance to retake the lead when Troost-Ekong headed a free-kick from Ademola Lookman wide, but the decisive moment came from an inspired finish by Haller when the Borussia Dortmund man stuck out his right leg to flick Adingra's cross past Nwabali.
Fairy tale ending for Fae
Emerse Fae (far right, in white) coached Nice's youth teams and was the reserve team of French Ligue 1 club Clermont before becoming Ivory Coast's assistant coach in May 2022
The tournament, which was delayed from its intended staging in June and July last year because of weather concerns in West Africa, will live long in the memory after a record number of goals, unrelenting upsets and an apparent capacity for unceasing drama.
Much of that was provided by the hosts, who had appeared on the brink of an early exit after a shock 4-0 defeat by Equatorial Guinea in their final Group A outing.
Gasset departed as coach and Fae managed to instil renewed belief after inheriting a side which were given a second life as one of four best-ranked third-placed sides.
Progress had been secured after Morocco - whose national flag Ivory Coast co-captain Max Gradel waved before lifting the trophy - beat Zambia in the final round of group games to stop the southern Africans stealing their spot.
Elephants supporters had understandably been left reeling after what was a record defeat at home but rallied behind a side which showed incredible mental fortitude to eliminate Senegal and Mali in two epic ties, prior to a far more routine victory against DR Congo in the semi-finals.
Fae, who was part of the Ivory Coast side that finished runners-up to Egypt in 2006 - a campaign in which he played every minute, has now won Africa's biggest prize in just his fourth game in senior management.
The resilience of the 40-year-old's side was underlined as the hosts held their nerve after falling behind against the run of play in front of a sea of orange in the final.
Ivory Coast become the 12 host nation to win the Nations Cup title, while Nigeria will be left to rue a fifth defeat in the showpiece game - and their second in Abidjan after losing to Cameroon in