Keshi announced his decision to stand down on Monday, less than 24 hours after guiding Nigeria to their third continental crown with a 1-0 win over Burkina Faso.
It had been reported Keshi had a falling-out with Nigerian Football Federation (NFF) officials after they booked a flight home for the squad ahead of their quarter-final against tournament favourites Ivory Coast, a match they won 2-1.
However, following a meeting with Nigeria's Sports Minister Bolaji Abdullahi, he has been persuaded to carry on.
A statement from the NFF, labelled as being on behalf of Keshi, read: "My attention has been drawn to reports in the media that I have resigned my appointment as head coach of Super Eagles of Nigeria.
"While I have had cause to express my displeasure over some issues that happened in the course of our participation in the AFCON which my team won by the grace of God, especially concerning my relationship with the Nigerian Football Federation.
"I have since had opportunity to discuss the various issues with all concerned. I am therefore pleased to say that I have reconsidered my position and have decided to continue with my job.
"I want to thank the Honourable Minister of Sports, Mallam Bolaji Abdullahi, for his swift and kind intervention."
It is a remarkable about-turn from Keshi who on Monday told a South African radio station that he had quit.
The 51-year-old appeared on Metro FM, part of public broadcaster SABC, and said he had informed the NFF of his decision following the final.
Metro FM presenter Robert Marawa tweeted: "Stephen Keshi has just announced that he handed over his resignation letter after the game exclusively on 083Sport@6 With Marawa on MetroFM".
Keshi is only the second man to win the Nations Cup as a player and a coach - following Egypt's Mahmoud El Gohary.