The 80-year-old American filmmaker told a masterclass at the Cannes film festival late on Thursday that he was invited by the chief exorcist in Rome to record the event.
"I was invited by the Vatican exorcist to shoot and video an actual exorcism which... few people have ever seen and which nobody has ever photographed," he said.
Friedkin said he was taken aback at how close the ceremony was to the exorcism depicted in his 1973 film.
"I was pretty astonished by that. I don't think I will ever be the same having seen this astonishing thing.
"I am not talking about some cult, I am talking about an exorcism by the Catholic Church in Rome," he added.
But the Vatican denied "making any such invitation. The Vatican (itself)
does not have an exorcist," a spokesman told AFP.
Each Catholic diocese has an exorcist and papal universities regularly
organise training for the exorcism.
"People often confuse any Catholic initiative/organisation/person with the Vatican. Perhaps this is the case here," he added.
The director said he intended to shoot "The Exorcist" - based on a bestselling novel by William Peter Blatty - as a horror movie, but the more he learned the more it became a story of the supernatural instead.
While the book was based on the 1949 case of an American teenager called Roland, Friedkin said the Catholic "archdiocese of Washington DC asked Blatty to change the gender (in the novel) so as not to draw attention to the young man."
But in reality, the director said, "it was a young man of 14 years, not a girl" who was allegedly possessed.
The film recounts the demonic possession of a 12-year-old girl and her mother's attempts to win her back through a rite conducted by two priests.
Friedkin said he believed the boy was genuinely possessed. "I'm convinced that there was no other explanation. I read the diaries not only of the priest involved (in the exorcism), but the doctors, the nurses and the patients at Alexian Brothers Hospital in Saint Louis where this case was carried out," he added.
"Everything having to do with medical science and psychiatry was attempted. This young men suffered from afflictions very similar to what's in the film, as hard is that is to believe."
The exorcism scenes in the film has been repeatedly voted among some of the scariest ever shown in cinemas.
"When I started I thought I was making a horror film and then the priest, who was the president of Georgetown University (in Washington DC), let me read these diaries and I knew that it was not a horror film," Friedkin said. "This was a case of exorcism."
"I believed in this story," Friedkin told the audience in Cannes, referring to the original possession of the boy. "I made this story as a believer. I'm not Catholic, I don't to church, I don't belong to a church or a synagogue.
"I do believe in the teachings of Jesus," Friedkin added, whose parents were Jewish immigrants from Ukraine.
"I believe they are incredibly profound and beautiful and we know that this character existed... the supernatural aspect I leave to each person's conscience and belief system," he added.
"I don't intend to join a church and yet what amazes me... is the fact that this man (Jesus) over 2,000 years ago preached in the desert, on street corners and in synagogues and there is no recording of his voice, there is no words that he wrote... yet billions of people have believed in the idea of Jesus Christ.
"There must be something in there," said Friedkin, who also made "The French Connection", and was with Francis Ford Coppola and Peter Bogdanovich one of the leaders of the "New Hollywood" group of filmmakers in the early 1970s.