The shooting occurred right after mass at the Metropolitan Cathedral in Campinas, a city about 60 miles north of Sao Paulo, according to Wilson Cassante, a spokesman for the archdiocese.
He said the officiating priest had left before the shooting began.
A spokesman for Sao Paulo state firefighters said four injured people had been taken to local hospitals.
Their conditions were not immediately known.
Mr Cassante said church officials did not recognise the gunman or have any ideas about his motive.
"It's so sad," said Mr Cassante.
"It's hard to imagine the pain this has caused."
Hamilton Caviola Filho, a police investigator, told news portal G1 that authorities had reviewed surveillance footage from inside the cathedral.
The gunman "came into the church, sat on a chair, with time to think, and then got up and starting shooting", said Mr Caviola Filho.
The investigator also said that before shooting himself in the head, the suspect took a bullet in the ribs from responding police.
In total, the suspect fired at least 20 shots, said Mr Caviola Filho.
Images on Globo News showed paramedics taking bodies and injured from the church.
Firefighter Alexandre Monteiro told G1 that the four injured were in stable condition.
The motive was not clear.
Authorities have yet to release the name or age of the suspect.
While Brazil leads the world in total annual homicides, mass shootings are relatively rare.
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