Crews arrived at Our Lady of Guadalupe Church on the 1300 block of East Third Street at about 1:30 a.m.
The two-story north section of the church, which was being remodeled, was fully engulfed in flames.
Father Alfredo Dedios was awakened by the fire.
"I think maybe it was a nightmare or something like that," said Dedios. "I didn't believe it."
Firefighters put out the blaze, but they were concerned that part of the structure could collapse.
"There was a very large fire inside," said one firefighter. "This whole thing was pretty well going so that was our concern, about either the building collapsed or the scaffold around it and everything like that."
The section that was destroyed had been under construction for the last four months and it was just weeks from being completed.
"It's just sad to see what happened here," said one parishioner.
The main sanctuary, where mass is held, was salvaged as well as its contents.
There were no reports of injuries. The cause of the fire was under investigation, but officials say that it appears to be accidental.
Thousands of people attend mass at the church, which was founded in 1938.
"Total devastation" said parishioner Ralph Serrano. "I've attended this parish ever since 1964. So it's all my lifetime and stuff like that."
On Dec. 12, parishioners will celebrate the Lady of Guadalupe Feast as scheduled. Officials say the sanctuary will be used and tents will be set up in the parking lot.
Anyone with information about the fire is asked to contact the Santa Ana Fire Department at (714) 647-5700.