Police spokesman Micky Rosenfeld says two other Eritreans, including a pregnant woman, suffered smoke inhalation in Thursday's blaze.
Rosenfeld says police are searching for suspects and that "it seems to be that it was an attack, carried out deliberately."
This is the second suspected case of arson against migrants' homes in Jerusalem in recent weeks. Rosenfeld says no one has been arrested in the first case.
Tensions in Israel over the unsanctioned arrival of tens of thousands of African migrants have turned violent in recent weeks.
An estimated 60,000 Africans have slipped into Israel over the past seven years, through the border with Egypt.