FIFA, which suspended the West African nation over political interference in the sport on Monday, said the situation had improved and removed the ban until later this month.
Meanwhile, the Confederation of African Football (CAF) said that Sunday's match in Conakry would go ahead as planned.
Nigeria, who narrowly escaped an international ban in July over the government's threat to pull them out of international competition, beat Madagascar 2-0 in their opening group match last month.
FIFA said in a statement that the acting general secretary of the Nigerian federation (NFF) had been allowed to return to his post and the government had stopped its interference in the Nigerian League.
The world governing body said there had also been assurances that a court case involving the NFF would be dropped. It set October 26 as the deadline for that to be confirmed.
"However, should the NFF still be embroiled in court actions or any other issue preventing it from working freely on that date, the suspension will be automatically confirmed until all problems have been definitively solved," added FIFA.
LATEST CHAPTER
The incident was the latest chapter in the chaotic administration of Nigerian football in which national team coaches are hired and fired with astonishing regularity and directors and politicians are continually fighting.
Nigeria were also banned by the Confederation of African Football (CAF) in 1996 when then President Sani Abacha withdrew the team from the African Nations Cup finals in South Africa because he had been criticised by Nelson Mandela over the judicial execution of political opponents.
As a result, Nigeria missed the following Nations Cup in Burkina Faso in 1998.
Nigeria have played at the World Cup four times, twice reaching the last 16, and won the Nations Cup twice but many feel it is a disappointing record for such a populous, football-mad country.
Nigeria were knocked out in the first round at the World Cup in South Africa after failing to win a game, prompting President Goodluck Jonathan to order the team's withdrawal from international football for the next two years.
As FIFA threatened to suspend the Nigerian federation, Jonathan reversed his decision after the federation agreed to disband the team and after appeals from Nigerians including former leaders.
