Fifa had given Nigerian authorities until 12 noon on Monday to resolve the leadership tussle inside its football governing body.
At 11.38am, a few minutes before the deadline, Laolu Akande, Special Assistant to Vice President Yemi Osinbajo, announced on Twitter that the government recognised the Pinnick-led executive as the authentic leadership of the Nigeria Football Federation (NFF).
The FG has already conveyed to FIFA its firm position recognizing Amaju Pinnick-led NFF as the current & only NFF Exco. Govt will also continue to work with all relevant stakeholders involved to resolve dispute in a timely manner. FG is upholding NFF treaty obligations to FIFALaolu Akande (@akandeoj) 20 août 2018
Pinnick has been engaged in a legal battle for the leadership of the NFF with his rival Chris Giwa since a contested election in 2014.
Giwa was declared the winner of the election, which was held in Abuja on August 26 of that year, while Pinnick won a second poll that was conducted the following month in Warri.
After Giwa took over control, world football governing body Fifa faulted the move, slapping him with a five-year ban for breaching its code of ethics. The body then announced that it recognised Pinnick as the NFF president.
The Fifa ban on Giwa was seemingly disregarded by Nigeria's Supreme Court, which recognised him as the true NFF president.
Sports Minister Solomon Dalung later directed the football federation to comply with the court ruling.
Nigeria has a long history of being threatened with Fifa sanctions for government or court interference in NFF affairs.
The dispute now appears to be over, to the delight of Super Eagle fans, who had feared they might miss out on next month's qualifiers for the African Cup of Nations.