At least 37 had died in the state of state of Minas Gerais and nine more in neighbouring Espirito Santo, according to local disaster officials, who said 28 people remained missing.
Some 20,000 people had been evacuated due to the threat of floods and landslides.
The capital of Minas Gerais state, Belo Horizonte, recorded 171 millimetres in one 24-hour period from Thursday to Friday, the highest rainfall in 110 years.
State Gov. Gustavo Zema declared a state of emergency in 47 cities, a measure meant to facilitate federal disaster aid.
He also decreed three days of official mourning for those killed in the floods and landslides.
Authorities in Espirito Santo said they were on maximum alert“ due to the forecast of more rain for Sunday.
In the city of Alegre, officials warned that a dam was in danger of breaking and urged people living below to evacuate.
Another 2,000 people were evacuated in the Rio de Janeiro state city of Itaperuna.