The doctor, identified as Ameyo Stella Adadevoh, a senior consultant endocrinologist, died in an isolation facility at the Yaba Mainland General Hospital in Lagos, Minister of Health, Onyebuchi Chukwu, said in a statement.
Medical sources said she had contracted the infection while treating Liberian-American Patrick Sawyer, adding that she was in coma before her death on Tuesday.
"Two other patients currently under treatment in the isolation wards are stable and are being taken care of," Chukwu said in a statement made available to Xinhua, noting that all fatalities recorded so far were of people who had close contact with Sawyer.
According to the official, the deceased doctor was one of the primary contacts of the Ebola virus disease case. The doctor's death takes the total number of Ebola fatalities in Nigeria to five.
The doctor died in an isolation facility in Lagos
The first was the death of Sawyer July 25.
A nurse who had attended to the Liberian died Aug 5. Jatto Asihu Abdulqudir, a 36-year-old staff of the Economic Community of West African States was killed by the virus last Tuesday. Another nurse also died of Ebola Aug 14.
At least 177 persons are under surveillance in the West African country, the government said.
Earlier this month, Nigerian president Goodluck Jonathan declared a national emergency, saying that a sum of 1.9 billion naira ($11.6 million) would be released to prevent further spread of the epidemic.
Ebola spreads through contact with bodily fluids of people infected by the disease.
According to figures released by the World Health Organisation (WHO) Tuesday, the number of Ebola cases in Guinea, Liberia, Nigeria and Sierra Leone, has reached 2,240 and a total of 1,229 deaths have been registered.
The current outbreak of Ebola virus disease began in Guinea in December 2013, leading to an epidemic in West Africa after it spread to Liberia, Sierra Leone and Nigeria.