This follows after the patient was showing potential symptoms of the disease after working in Guinea and Sierra Leone.
The South African woman, whose identity was not revealed, flew in to Lagos airport from Morocco. She was being treated as a suspected case and was being taken to Lagos' Ebola treatment center for tests to see whether she actually had the virus.
The traveller, who lives in Cape Town, filled out a health questionnaire on her arrival at Lagos in which she acknowledged suffering from diarrhoea and vomiting, both possible symptoms of the Ebola haemorrhagic virus.
(READ MORE: UPDATE: S.Africa tests possible Ebola victim )
Around 2,300 people have died so far this year in the worst Ebola outbreak on record which has mostly affected Liberia, Sierra Leone and Guinea. It has also reached Nigeria and Senegal because of sick travellers "importing" the disease. Democratic Republic of Congo has a separate outbreak.
"This person has been in Guinea and Sierra Leone since April ... she has symptoms," Dr. Morenike Alex-Okoh, director of Port Health Services at Lagos airport, told Reuters. The testing process was likely to last a few days.
(READ MORE: S.Africa imposes ban on Ebola-affected countries)
Nigeria, Africa's most populous nation, has instituted Ebola screening, including infra-red temperature scans and symptoms checks, at its airports and ports after a Liberian-American infected with the disease brought it to Lagos in July after flying from Liberia. His is one of seven deaths recorded so far out of 19 confirmed cases in Nigeria.
"Nigeria cannot afford another 'importation' (of Ebola)," said Dr. Aileen Marty, a professor of infectious diseases at Florida International University College of Medicine.
(WATCH VIDEO: Update on Nigeria's Ebola status)
Marty is working with Nigerian health authorities, under the auspices of the World Health Organization (WHO), to maintain port of entry Ebola checks across the African oil producer.
She told Reuters the fact that the South African traveler displayed several Ebola-like symptoms and had been in the high-risk zone justified her being treated as a suspected case. But such symptoms are also present in other diseases, such as malaria and cholera, hence the need for a specific Ebola test.