Lagos University Teaching Hospital said the two died this week after being admitted for treatment.
"Each of these two patients presented very late and died in spite of efforts to salvage them," Professor Chris Bode, the hospital's chief medical director, said.
The first case was a 39-year-old pregnant woman with a bleeding disorder who died after stillbirth, he said.
A post-mortem examination had been conducted before her Lassa fever status was confirmed.
He said a doctor who took part in the autopsy and was confirmed with the disease, was responding to treatment.
Bode said two other suspected cases brought to the hospital were awaiting the results of tests.
He urged health workers to maintain "a heightened level of alert" and observe every precaution in handling suspected cases.
Lassa fever, also known as Lassa hemorrhagic fever, belongs to the same family as Marburg and Ebola, two deadly viruses that lead to infections with fever, vomiting and in worse case scenarios, haemorrhagic bleeding.
More than 100 people were killed last year in one of the nation's worst outbreaks of the disease, affecting 14 of the 36 states, including Lagos and the capital Abuja.
The virus is spread through contact with food or household items contaminated with rats' urine or faeces or after coming in direct contact with the bodily fluids of an infected person.
Nigeria's Centre for Disease Control (CDC) in Abuja confirmed the outbreak.
"We have put health workers on the alert and are working with the authorities in Lagos to contain its spread," an official said.
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