Health minister Onyebuchi Chukwu said the medic died on August 22 after treating a patient who had contact with Liberian-American Patrick Sawyer, who brought the virus to Nigeria and who died in a Lagos hospital on July 25.
"Following the report of this death by the doctor's widow the next day, the case had been thoroughly investigated and laboratory analysis showed that this doctor died from EVD (Ebola Virus Disease)," he told reporters in the capital Abuja.
The latest case brings to six the number of people who have died from the haemorrhagic fever in Nigeria. Fifteen people have now been confirmed to have the disease. On Wednesday, Chukwu had said that the virus was contained as there were no cases outside Lagos but warned against complacency in fighting the disease.
News that a doctor died 435 kilometres (270 miles) away will raise fears about the spread of the virus, just as Nigerians began to think that they had stopped Ebola in its tracks.
Port Harcourt, the capital of Rivers state, is the centre of Nigeria's oil industry and home to a number of oil giants, including Anglo-Dutch giant Shell, France's Total and US firm Chevron.
Nigeria is Africa's largest oil producer, churning out roughly two million barrels a day, with crude accounting for more than 90 percent of its foreign exchange earnings.
Residents in Port Harcourt said they were shocked and scared by the arrival of Ebola and called on the state government to tackle the virus.
"Port Harcourt plays host to a lot of people, including foreigners. All efforts should be made to check the spread of the virus," said local student Lucy Ekeh.
Chukwu said the patient, an official with the ECOWAS regional bloc who took Sawyer to hospital after he arrived unwell at Lagos airport on July 20, managed to evade detection and went to Port Harcourt in the last week of July.
Another ECOWAS official died of Ebola, the bloc announced on August 12.
His colleague saw the doctor who died in Port Harcourt in a city hotel room after showing Ebola-like symptoms, Rivers State health commissioner Sampson Parker said separately.
Chukwu added: "After four days, following a manhunt for him, he (the patient) returned to Lagos by which time he was found to be without symptoms.
"This case would have been of no further interest since he had completed the 21 days of surveillance without any other issue but for the fact that the doctor who treated him died last Friday."
Following the doctor's death, the minister said that several contacts had now been "traced, registered and placed under surveillance".
His widow, also a medical doctor, has shown symptoms of the virus and has been placed in isolation pending results of laboratory tests, he added.
"We don't know what the result will turn out to be but certainly if it turns out to be positive, it's likely we will move her to Lagos," the minister said.
Chukwu said that there were 70 people under surveillance in Port Harcourt, while six people were being watched in the eastern city of Enugu, where a nurse who treated Sawyer visited before displaying symptoms.
A treatment group has been in Port Harcourt since Wednesday morning and a mobile laboratory was being sent to the city this weekend, he added. Parker said that the hotel had been decontaminated.