Nigeria were already assured of a place at the 2025 Africa Cup of Nations before the players even kicked a ball in anger against Benin Republic in Abidjan on Thursday.
A goal from Fahd T. Saad Mohamed in the 84th minute gave Libya a shock 1-0 win over Rwanda in the other group fixture.
The Super Eagles points tally had been boosted by the decision of the Confederation of African Football CAF to award them three goals and three points after the debacle in Libya.
The Match Day 4 game, which was scheduled to be played in Benina on October 15, was called off after the Nigerian delegation saw their flight diverted.
They were then held hostage in an abandoned airport for at least 17 hours.