The blaze broke out Saturday afternoon in the engine room of the Comandante Ferraz station on King George Island, where 32 civilian researchers and 12 sailors are stationed, CNN reported.
Along with the deaths, another sailor was injured battling the blaze, the report said.
The cause of the fire wasn't immediately known, but military police were investigating, navy Adm. Julio Soares de Moura Neto told Brazilian media.
The state-run news agency Agencia Brasil said contingents from Argentina, Chile and Poland helped evacuate the survivors to a military base in southern Chile.
The station was used to study climate change, marine life and the atmosphere and will be rebuilt, Defense Minister Celso Amorim said.