Chris Giwa claimed to have been elected the new president of the NFF following a general assembly last month.
FIFA did not recognise the result of the ballot, however, as current president Aminu Maigari was being held for questioning while the vote was taking place.
The FIFA Emergency Committee subsequently set a deadline of September 8 to remove those claiming positions in the NFF that were not recognised by FIFA and restore the Maigari-led committee and, if those requirements were not met, the NFF would be suspended.
However, the Confederation of African Football has now released a statement confirming that the NFF have met those demands and will avoid a ban - meaning Nigeria are free to play their Africa Cup of Nations qualifier with South Africa on Wednesday.
"In a letter dated 9th September, addressed to the president of the Nigeria Football Federation, Aminu Maigari, the secretary general of FIFA, Jerome Valcke noted the return to normalcy in the Nigerian Football Federation and compliance with conditions prescribed by the emergency committee of FIFA of September 3. The NFF is accordingly not suspended," the statement read.
"This return to normality, as indicated in the correspondence from the president of the Nigerian federation to FIFA in a letter of 8th September has been noted together with the reinstatement and return to work at the association headquarters in Abuja of the NFF president and staff to work without hindrance.
"The secretary general of FIFA also noted that people who claimed to have been elected to preside over the affairs of the Nigerian federation evacuated the premises of the institution."
The statement added a list of FIFA recommendations, which read: "The correspondence of the secretary general of FIFA is accompanied by recommendations including the need for the urgent holding of an executive committee and a general assembly of the NFF and defining and adopting the roadmap for NFF elections as soon as possible.
"These should all be done be in accordance with the rules and regulations of the Nigerian federation.
"FIFA further cautioned that should the electoral process be affected by any interference or occurrence of any mishap, the case would be referred again - and without prior notice or warning - to the appropriate FIFA bodies for immediate suspension of the NFF until the next FIFA Congress."
FIFA had previously suspended the NFF in July, with government interference following Nigeria's poor performance at the World Cup cited as the reason for the sanction.
