The incident happened at St. Timothy's United Methodist Church in Stone Mountain.
Police told Channel 2 Action News reporter Erica Byfield on Sunday that the woman continued to recover at a local hospital.
Church members told Channel 2 Action News reporter Tony Thomas that they believe the attacker was a stranger.
The attack occurred in the middle of the afternoon as a woman worked alone inside the church.
"Everyone is shocked, but we just believe we will come together to support each other and pray for God to bring healing and a miracle," said one parishioner, who did not want to be identified.
Crime scene tape blocked the entrance to the church office and special victim's unit detectives worked inside the church Saturday night. Police have said very little about the attack, but officers said they were called to the Memorial Drive church just after 3 p.m. Saturday. A person who was working alone in the church said she was attacked by a lone man.
Another woman, who also did not want to be identified, found the injured woman.
She told Thomas she believes the woman was attacked by a stranger. "That's what the police are intimating. That's what we think," she said.
DeKalb County police did confirm the woman was sexually assaulted.
"We did have a victim inside, the number of victims I'm not going to be able to say," said Sgt. J.M. Love of the DeKalb County Police Department.
Church members gathered at the church Sunday morning to pray for their friend and hoping detectives catch the man responsible.
On Sunday, police said they were looking for a black male with short hair in his 50s.