Archbishop Emmanuel Milingo of Lusaka spent about 30 minutes inside the pope's residence at Castelgandolfo outside Rome.
"The meeting opens dialogue which, we hope, will lead to positive developments," said Father Ciro Benedettini, a Vatican spokesman.
Milingo has been ordered to separate from his wife, South Korean doctor Maria Sung, whom he married in a mass wedding ceremony officiated by the Reverend Sun Myung Moon of the South Korean Unification Church May 27.
In a letter sent to the pope, and made public three weeks ago, the archbishop said he had not married for lust.
"I have not married for concupiscence. At the age of 71, sexual impulses are reduced to a minimum.
"I married with God in mind, and was pushed by a deep desire to renew pure and honest faith, denouncing serious sins in the moral domain which have hurt and weakened the Catholic clergy," Milingo wrote.
Following the marriage, Vatican spokesman Joaquin Navarro Valls said Milingo could no longer "be considered a bishop of the Catholic church."
The Roman Catholic church has also said Milingo faces sanctions -- though the word excommunication has not been used -- if he does not cut his ties with the activities of the Unification Church by August 20.
In threatening further sanctions last month, Vatican officials said they had been unable to contact the archbishop since his marriage.
The Catholic church does not allow its clergy to marry.
Even before his marriage, Milingo had repeatedly angered the Vatican for working as a healer and exorcist.