It was the first meeting between the Pope and the Archbishop, Dr Rowan Williams, since the Vatican initiative.
The archbishop, who is head of the 70 million-strong worldwide Anglican Communion, has said he does not believe the initiative will harm relations.
Some Anglicans have accused the Pope of interfering at a sensitive time for the Church of England.
The Vatican says its invitation came in response to pleas from Anglicans unhappy about the creation of women bishops.
BBC Rome correspondent Duncan Kennedy said: "The way the commentators are looking at this is that it is good the two men are talking, but really one meeting is not going to resolve the differences between the two sides over these really large issues that separate them."
Dr Williams has signalled he would like to build a new relationship, emphasising shared fundamental beliefs rather than "negative" secondary issues such as women clergy, our correspondent added.
Another cause of discord in the worldwide Anglican communion has been the election of an openly gay bishop and the blessing of same-sex unions.
Under the terms of the Pope's proposed Apostolic Constitution, groupings of Anglicans would be able to join "personal ordinariates".
This would allow them to enter full communion with the Catholic Church, which has more than one billion members worldwide, but also preserve elements of the Anglican traditions.
The first English clergy could convert early next year.
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