Moon, who was hospitalised with complications from pneumonia more than two weeks ago, died shortly before 2:00 am (1700 GMT Sunday) at a hospital in the church's headquarters in Gapyeong, east of Seoul.
Revered by his followers but denounced by critics as a cult-building charlatan who brainwashed church members, Moon was a deeply divisive figure whose shadowy business dealings saw him jailed in the United States.
His church, which he built into a global religious movement, was best known for organising mass weddings that married thousands -- sometimes tens of thousands -- of identically-clad couples in sports stadium ceremonies.
The couples often met for the first time on their wedding day after being personally paired up by Moon -- despite often being of different nationalities and having no common language.
The church claimed its members -- mocked as "Moonies" by the media -- totalled three million at the time of his death, although some experts say numbers had fallen sharply from a peak in the 1980s to just several hundred thousand.
"He was our father and God's messiah. His body was custom-made by God so we believed he would live until 100," Moon's close aide Bo Hi Pak told reporters in Gapyeong.
"Now with him gone to heaven, all of us are tremendously saddened. We are in the deepest sorrow," a tearful Pak said.
Moon had been on life support since Friday after suffering multiple organ failure.
A church statement said Moon's body would "lie in state" for 13 days prior to his funeral on September 15.
Born to a farming family in 1920 in what is now North Korea, Moon said he had a vision aged 15 in which Jesus asked him to complete his work on Earth.
Rejected by Korean Protestant churches, he founded the Unification Church in 1954 -- a year after the Korean War.
As the church rose to prominence in the 1970s and 80s, spreading to the United States, it spawned a multi-billion dollar business empire encompassing construction, food, education, the media and even a professional football club.
Media holdings include the Washington Times newspaper and United Press International news agency, and it also dominates the fishing and distribution industry supplying sushi outlets in the United States.
A church-affiliated firm, Pyeonghwa (Peace) Motors, established a joint car-making business in North Korea in 1999.
Throughout his life, Moon assiduously courted political leaders in what critics said was a bid to lend legitimacy to his church which has been condemned as heretical by some Christian organisations.
Despite his hardline anti-communist stance, he travelled to North Korea in 1991 to meet then leader Kim Il-Sung to discuss reunification of the divided peninsula.
There was no official comment from either North or South Korea on Moon's death.
The teachings of the Unification Church are based on the Bible but with new interpretations, and Moon saw his role as completing the unfulfilled mission of Jesus to restore humanity to a state of "sinless" purity.
Moon's emergence as a significant religious leader was tainted by legal problems.
Having moved to the United States in 1972, he was indicted on tax evasion charges in 1981 and served 11 months in prison.
Moon, who returned to live in South Korea in 2006, was admitted to a Seoul hospital in mid-August this year before being shifted to the Gapyeong estate after his kidneys ceased to function.
There was no mass mourning early Monday at the huge, mountain-ringed compound which comprises dozens of modern facilities including schools, a hospital and training centres.
But followers left numerous grief-stricken messages of loss on the church's official website.
"I feel like the sky is falling and the whole world has collapsed," wrote one.
At the movement's main church in Seoul, a handful of worshippers read a special edition of the church-affiliated newspaper on Moon's death.
Yamanaka Katsuyo, a Japanese follower who married a South Korean man at a mass wedding in Seoul in 1988, said she was devastated by the death of the man she credited with "changing my entire life".
"He picked a husband for me and we have lived happily ever after with three children," she said.
Moon had 14 children with his second wife, Hak Ja Han. Hyung Jin Moon, the youngest of his seven sons took over as the church's top leader in 2008 at the age of 28.
In signs of a possible family rift, another son reportedly filed a lawsuit against his mother last year seeking 23.8 billion won (US$22.3 million) allegedly sent to the church's missionary foundation without his permission.
The court ruled the money was a loan but ordered it be returned, the Yonhap news agency said.
