Nigeria's health minister, Onyebuchi Chukwu, said the "patient was subjected to thorough medical tests ... which confirmed the virus of Ebola," as the cause of death.
The man, who collapsed on arrival at the airport on Thursday, was kept in isolation and had not entered the city, the official earlier told Reuters.
Paul Garwood, of the World Health Organisation, said the victim left his home nation with no symptoms, but reported feeling unwell on arrival in Lagos.
Ebola has killed 660 in West Africa, with the number of cases surpassing 1,000, the WHO said in a statement.
Garwood said that the extent of what is the deadliest outbreak of Ebola on record was still emerging.
"This is a trend, an overall picture. It's hard to get an exact picture on the scale of the situation at the moment," he said.
The UN health agency said 28 new deaths were recorded between July 18 and July 20.