They then lashed out at them with machetes, doused them with flammable liquid and set fire to them with a blow torch.
At least one person - an Irish nun - was killed in the attack at the Cathedral of the Immaculate Conception in Castries. Thirteen others were injured. The Caribbean News Agency (Cana) reported on Monday that one of them had died in hospital.
Witnesses said a group of three or four men entered the church on Sunday as worshippers were lining up to receive Holy Communion.
They then lashed out at them with machetes, doused them with flammable liquid and set fire to them with a blow torch.
Prime Minister Kenny Anthony condemned the attack as sick and demonic, and vowed to punish those responsible.
Police spokesman Albert Fregis said St Lucia's Rastafarian leaders had also denounced the attack.
Vestments alight
An Irish nun who survived the assault has described the scenes of horror in what she called the "Satanic" incident.
"They were spraying people with kerosene, and then torching them."
The nun who died, 72-year-old Sister Theresa Egan, originally from Co Laois, was serving communion and was hit in the head by one of the machetes.
"I saw the priest who had been saying mass come out of the church with his vestments alight," Sister Mel told Irish Radio.
"I saw Sister Theresa fall to the ground and I wanted to help her. But I then felt a terrible force on the side of my head and also fell and could not move.
"It was Satanic, and a totally new departure. People here are very angry."
The priest, the Reverend Charles Gaillard, is said to be critically ill with burns.
Reports say the two suspects told police they were prophets sent by Haile Selassie, the late Ethiopian emperor worshipped as a god by Rastafarians.
There are conflicting reports from St Lucia as to whether the men belonged to an anti-Christian organisation.
Lined up
Some church officials have been quoted as saying anti-Christian symbols were posted on the doors of Cathedral of Immaculate Conception and other churches last week.
More than 400 were in the cathedral at the time of the attack.
Worshippers held captive one suspect, named as Kim John, and police found a second one hiding in bushes nearby. They are still looking for at least two other suspects.