The cancellation follows an airport ordeal in Libya, where Nigerian players and officials were detained for several hours at Al Abraq Airport under unclear circumstances.
The Nigerian contingent was stranded when their flight, initially bound for Benghazi, was unexpectedly diverted.
Despite the Nigerian Football Federation arranging transport in Benghazi, Libyan authorities allegedly failed to provide buses for the team at Al Abraq.
CAF have confirmed that the highly anticipated second-leg clash between Nigeria and Libya will not proceed as planned.
The African governing body confirmed on Monday that the incident is under investigation, and the matter has been referred to the Disciplinary Committee for further review and a final decision.
While no date has been set for the rescheduled match, CAF's intervention suggests a resolution could be imminent.
Nigeria currently lead Group D with seven points, followed by Benin with six points, while Rwanda sit third with two points and Libya are at last with one point.
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