But he continued to perform healings at well-attended public ceremonies that brought him a following in Europe.
Archbishop Emmanuel Milingo opens himself up to excommunication by going through with the ceremony.
The bride - identified as Sung Ryae Soon, from South Korea - was chosen for him earlier in the week, said a spokesman for Moon's movement.
Archbishop Milingo said God was the inspiration for his decision to marry, in defiance of Church doctrine which requires priests to be celibate.
"After a lifetime of devotion to the Church and to my priestly vows, the Lord has called me to take a step that will change my life forever," he said in a statement before the ceremony.
Forced out
The maverick Catholic was archbishop of Lusaka, Zambia, until 1983, when he resigned under pressure from Rome - an almost unprecedented event.
The Vatican objected to allegations that he carried out faith healings and exorcisms and brought him to Rome to make it easier to keep an eye on him.
But he continued to perform healings at well-attended public ceremonies that brought him a following in Europe.
Last year, the Vatican issued new guidelines on exorcism that were widely understood to be aimed at Archbishop Milingo.
He was quietly retired from his position at the Pontifical Council for Pastoral Care of Migrants and Itinerant People last year.
A Vatican spokesman declined to comment on his marriage "until we hear something directly from Milingo".
He has appeared at group weddings conducted by the Rev Moon in the past two years.
Return to Africa
Archbishop Milingo said he and his wife would move to Africa to continue his mission.
"I am and always will be devoted to the Church that I love," he said.
Former Catholic priest George Stallings, an American, also married at the ceremony on Sunday.
He was excommunicated in 1990 for founding the African American Catholic Congregation, which he now leads.
The Rev Moon personally arranges many of the pairings at the mass weddings that are a central part of the church he leads.
His followers believe that the "Lord of the Second Advent" will appear at the end of time with his wife to complete the redemption begun by Jesus.
According to the teaching of the 81-year-old Korean-born Reverend Moon, the second messiah was born in Korea around 1920.
The Rev Moon has lived in the United States since 1973, and controls a network of non-profit organisations and businesses.