The service ended two weeks of mourning during which 200,000 people attended wakes across the country, CNN reported.
Moon died Sept. 3 at age 92 after he developed complications from pneumonia.
More than a dozen pallbearers dressed in white military-style uniforms carried his red casket through a church filled with flowing flower arrangements, up red-carpeted stairs to an elevated altar.
The eulogy was presented by the Rev. Hyung Jin Moon, the founder's seventh and youngest son, and his father's successor.
Hyun Jin, Moon's third and oldest living son, did not attend the service but said a separate memorial for his father would be held in the United States, Yonhap News Agency reported.
Hyun Jin, 43, is chairman of the Unification Church International but is embroiled in a legal dispute with the church. He lives in the United States. UCI owns United Press International.
Sun Myung Moon had been a controversial religious figure during much of his ministry, The Daily Telegraph said.
He founded his church in 1954, but was rejected by mainstream Protestant churches when he claimed to be a messiah sent by God to complete Jesus' work.
Moon was famous for officiating at mass weddings where he married hundreds, and sometimes thousands, of couples. He also served a prison sentence in the United States for tax evasion.