The perpetrator's first victim is said to have been a 70-year-old woman who was in the church.
After cutting her throat with a knife, he turned on Vincent Loquès, 54, whom he killed.
The third victim was Simone Barreto Silva, 44, from Brazil but living in France for 30 years.
She managed to escape to a nearby cafe after the attack.
There she died of her injuries.
President Emanuel Macron has called the incident an Islamist terrorist attack.
The identity of the 70-year-old woman has not yet been reported.
A "good living"
The father of two, Vincent Loquès, had opened the gates of the church every day since 2013. He would have turned 55 the day after the terrorist attack.
Acquaintances and colleagues with whom the magazine Le Parisien spoke describe him as a sympathetic and orderly person - a "bon vivant", outgoing and pleasant.
Two churchgoers resemble the church at his living room.
- He was always there.
He was not only a watchmaker, he was the handy one.
The candles were always on, says one of the people to the newspaper.
Vincent Loquès' memory is also honored by a former pastor of the church.
- He was generous, reliable and had a strong character, says the priest Jean-Louis Giordan to Le Parisien.
Friend: Be a believer but tolerant
Simone Barreto Silva worked in geriatric care and has three children.
The Brazilian Foreign Ministry has expressed its sorrow over the incident, condemned the act and promised to stand up for freedom of expression worldwide.
- She was a brave, generous and deeply believing woman, but also tolerant, says one of her close friends to BFMTV.
- You were a woman so full of dreams and vitality, writes one of her relatives on Facebook, according to The Guardian.