An extraordinary general assembly of the federation went ahead in Abuja on Saturday despite FIFA's warning of a possible suspension for the African nation if it did not restore the old leadership to power.
A regional high court had earlier this week ordered the dismissal of the Nigerian Football Federation (NFF) executive, just over a day after the Super Eagles were eliminated from the World Cup by France in the last-16 on Monday.
The court also mandated the sports minister to appoint a caretaker administrator, who swiftly called new elections.
NFF president Aminu Maigari was also detained by police on Friday on his arrival back from Brazil but later released.
FIFA said on Friday that if the NFF leadership were not restored to their posts by next Tuesday the country could be suspended from all international football activities.
It warned against outside interference in the running of its member associations.
But Saturday's assembly endorsed the sacking of Maigari and his executive and the termination of the employment of all management staff at the NFF.
"The Congress bemoaned the unfortunate incident of the international embarrassment caused by failure of the Aminu Maigari-led NFF to fully and firmly resolve issues of finance with the Super Eagles ahead of the championship," a statement obtained by Reuters said afterwards.
Nigerian players were involved in strike action after winning through their opening round group to the last 16 at the World Cup in Brazil but resumed training after Nigerian president Goodluck Jonathan had spoken to several senior players by telephone and assured them their bonus money would be paid.
There is no clarity about who or why the court order seeking the dismantling of the NFF was brought but the swiftness of the injunction, the call for new elections and the assembling of the NFF electorate suggested a well orchestrated putsch.
African governments for decades dictated the leadership of their individual football associations until FIFA brought in the sanction of suspension for those interfering.
Drastic changes like those affected by Nigeria are now rare but fellow World Cup finalists Cameroon are being run by a 'normalisation committee' after their old executive was drummed out of office and their federation president jailed on fraud charges.
- Sports & Recreation
- Super Eagles