The one-tonne cow was grazing on a hill behind the small house, in the town of Caratinga, when it stepped onto the asbestos roof, which collapsed under its weight.
Joao Maria de Souza, 45, was lying in bed when the animal fell on him.
He was taken to hospital and died the day after, reportedly of internal bleeding.
Mr Souza was conscious and appeared to be in a good condition, but he had to wait too long to be seen by a doctor, relatives said.
Local media says this is the third such incident in the region in the past three years.
There were no casualties in the two previous incidents.
In the first occasion, there was no one inside the house when the cow fell through the roof.
In the second incident, a baby and a small child were sleeping next to the spot where the animal fell, in what was described at time as a miraculous escape.
Caratinga is in a hilly area of Minas Gerais, a Brazilian state traditionally known as a cattle raising and dairy producing region.