The sport's global body had said that, in response to state meddling in the running of the Nigerian Football Federation (NFF), it would suspend the country from international matches at 1100 GMT, thereby excluding the side from next month's African Nations Cup qualifiers.
FIFA said it had received confirmation that its recognised leadership team under Amaju Pinnick had been "given back effective control of the NFF and its offices".
"The suspension of the NFF will not take effect," it said in a statement more than three hours after the deadline passed.
Pinnick, elected NFF head in 2014, was in a stand-off with Chris Giwa, who had appealed against the election result and, after a protracted legal battle, won a favourable high court ruling in June.
Giwa was handed a five-year ban by FIFA for breaches of NFF statutes and the FIFA code of ethics in February 2017.
In a tweet posted at 1038 GMT, a spokesman for Vice President Yemi Osinbajo said Nigeria had "already conveyed to FIFA its firm position recognising Amaju Pinnick-led NFF as the current & only NFF Exco (executive committee)."
The government would work with all stakeholders "to resolve (the) dispute in a timely manner," he added.
Giwa previously appeared to have the backing of the government. He was included by Sports Minister Solomon Dalung on a proposed list of delegates to meet FIFA president Gianni Infantino in Zurich last week – an approach that FIFA rejected.
FIFA, which does not accept third party involvement in its member federations, and had given Nigeria a final warning on 14 Aug to ratify Pinnick's leadership.
In its statement, FIFA said it "will continue to closely monitor the situation in order to ensure that FIFA's rules and regulations are fully adhered to."
Nigeria are due to play a qualifier for the 2019 African Nations Cup in the Seychelles on Sept. 8.
(Reporting by Angela Ukomadu in Lagos, Mike Oboh and Abraham Achirga in Abuja and Michael Shields in Zurich; Writing by Paul Carsten; editing by John Stonestreet)
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