The case has prompted a scramble by authorities in Africa's most populous country who are now trying to trace everyone who arrived on the same flight as the patient and identify the places he visited before going to the hospital.
"We have started working to identify all the contacts of the person since he entered Nigeria and even those who were with him on the aircraft," Health Minister Osagie Ehanire told reporters on Friday in Nigeria's capital, Abuja.
The Italian, whose country is the worst-hit in Europe by the coronavirus outbreak, arrived on February 24 on a Turkish Airlines flight that had a connection in Istanbul, Akin Abayomi, Lagos state commissioner for health, told reporters.
After spending the night in a hotel near the airport, he arrived in the neighbouring state of Ogun on February 25 at his place of work.
He stayed there until he developed a fever and body aches on the afternoon of February 26, Abayomi said.
Health practitioners with his company then contacted biosecurity authorities, who transferred him to a containment facility in Yaba, Lagos state.
"It was very astute of the medical practitioners in that facility to keep him overnight in an isolated environment," Abayomi said.
Ehanire said the infection was confirmed on February 27 by the Virology Laboratory of the Lagos University Teaching Hospital, part of the Laboratory Network of the Nigeria Centre for Disease Control, and that the man is now quarantined but doing well.
As well as being the first in Nigeria, the patient is the first confirmed coronavirus case in sub-Saharan Africa.
Turkish Airlines did not immediately comment on the case. There are no confirmed cases in Turkey.
The World Health Organization has said it already has experts on the ground in Nigeria, which it identifies as one of 13 "high priority" countries in Africa.
In a sign of mounting concerns in Kenya, the country temporarily suspended flights from China on Friday. Kenya has no confirmed cases of the virus.