The gunman injured four more people before being wounded in a firefight with police and then shooting himself in the head, authorities said.
The shooting happened right after the midday service had ended at the Metropolitan Cathedral in Campinas, a city around 100km (60 miles) north of Sao Paulo.
Hours after paramedics were seen taking bodies out of the church, the gunman was identified as 49-year-old Euler Fernando Grandolpho, from Valinhos, a nearby city in the densely populated state of Sao Paulo.
Grandolpho, who worked as a systems analyst, was not a member of the church, authorities said.
He had held various jobs with government entities, including a stint as an assistant to the prosecutor in the public ministry in Sao Paulo, according to public records.
Authorities said they had not determined a motive.
A backpack found near the dead gunman had his identification but no note or other clues, police investigator Jose Henrique Ventura said.
“Thanks to the intervention of police, something much bigger was avoided,” Mr Ventura said, adding that the four injured were in stable condition.
Witness Danielle Coutinho told EPTV said she was sitting in the church chatting after Mass when the gunfire began.
A man sitting close to her was shot as others ran.
“I saw people getting shot. I can’t get it out of my head,” she said in tears. “It was horrible.”
Brazil is routinely the world leader in total homicides, though mass shootings are rare. Last year, nearly 64,000 people were killed.
President-elect Jair Bolsonaro campaigned on promises to crack down on violence, in part by loosening gun laws so more civilians could arm themselves.
Hamilton Caviola Filho, a police investigator said that authorities had reviewed surveillance footage from inside the cathedral.
The shooter “came into the church, sat on a pew, with time to think, and then got up and starting shooting,” he told news portal G1.
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