WHO representative Rui Gama Vaz, speaking in the capital Abuja, said it was a “spectacular success story”.
Nigeria won praise for its swift response after a Liberian diplomat brought the disease there in July.
The outbreak has killed more than 4,500 people in West Africa, mostly in Liberia, Guinea, and Sierra Leone.
An estimated 70% of those infected have died in those countries.
The WHO officially declared Senegal Ebola-free on Friday.
Meanwhile, European Union foreign ministers are meeting in Luxembourg to discuss how to strengthen their response to the threat posed by Ebola.
Speaking on the sidelines, French Foreign Minister Laurent Fabius said he expected the meeting to appoint a co-ordinator to galvanise the EU’s response to the epidemic.
“My colleagues are unanimous in saying that this idea of a European co-ordinator for the fight against Ebola is a good idea. The name will be chosen in the coming days. I think it’s a very important step.”
European countries have committed more than 500m euros (£400m; $600m) but the UK is pressing to double that amount.
Will Ross in Nigeria spoke to a doctor about how to treat the early stages
The money is being sought to help reinforce over-stretched healthcare systems in Liberia, Sierra Leone and Guinea and to mitigate the damage Ebola is doing to their economies.
Earlier, the Spanish government said a nurse who became the first person to contract Ebola outside West Africa had tested negative for the virus.
The result suggests Teresa Romero, 44, is no longer infected although a second test is required before she can be declared free of Ebola.
Ms Romero contracted the virus when treating two infected patients in a Madrid hospital.
Javier Limon, Teresa Romero’s husband: “I am very happy”
In another development, US health officials said 43 people being closely monitored after coming into contact with Ebola victim Thomas Eric Duncan had been given the all-clear.
They were subject to twice-daily monitoring during the 21-day incubation period.
However, others who cared for Mr Duncan remain at risk including two nurses he infected and their close contacts. Dallas Mayor Mike Rawlings said 120 people were still being monitored, with their waiting period due to end on 7 November.
The WHO can declare an Ebola outbreak over if two incubation periods of 21 days pass with no new cases. The last reported case in Nigeria – Africa’s most populous country – was discovered on 5 September.
“The virus is gone for now. The outbreak in Nigeria has been defeated,” WHO Nigerian representative Rui Gama Vaz said on Monday.
“This is a spectacular success story that shows to the world that Ebola can be contained but we must be clear that we have only won a battle, the war will only end when West Africa is also declared free of Ebola.”
The outbreak there began when Patrick Sawyer, an American-Liberian citizen, was diagnosed with the illness in July.
Nigeria declared a national public health emergency and Mr Sawyer later died of the disease, followed by seven Nigerians.
These included Dr Ameyo Stella Adadevoh, who diagnosed Mr Sawyer and is credited with helping to contain the outbreak at its source.
Dr Adadevoh’s son, Bankole Cardoso, told the BBC that because Mr Sawyer had been so quickly diagnosed, Nigeria was able to trace all those who could possibly have contracted the disease from him.
“That was probably the difference between us and our West African neighbours,” he said.
John Vertefeuille, from the US Centers for Disease Control and Prevention (CDC), said that Nigeria had taken the right steps to contain the outbreak.
“Nigeria acted quickly and early and on a large scale,” he told AFP news agency.
Nkosazana Dlamini-Zuma, who chairs the African Union Commission, told the BBC that countries affected by Ebola would have to deal with the consequences for years to come.
“A lot of things are almost at a standstill. They are not going to be producing as much food as they would have produced, they are diverting some of the money for education to other things to stamp out the epidemic,” she said.