The Vatican said the Pope had received Dr Rowan Williams in a private audience but gave no details.
An Anglican spokesman said the two spoke privately for about 20 minutes and discussed Christian-Muslim relations, inter-faith dialogue and the Pope's impression of his visit to the United States last month.
He described the visit, the second official meeting between the Pope and the spiritual leader of the world's 77 million Anglicans, as "warm and friendly".
In March, Cardinal Jean-Louis Tauran, the Vatican's top man for relations with Islam, criticised Dr Williams as mistaken and "naive" for suggesting that it was unavoidable that some aspects of Sharia law would be adopted in Britain.
Dr. Williams' remarks, in a speech in February, sparked a storm in Britain and beyond and became part of a broader debate on how to integrate Britain's 1.8 million Muslims.
He is in Rome for the 7th Building Bridges Seminar, an annual meeting of leading Christian and Muslim scholars for intensive study of biblical and Koranic texts.
The theme of this year's seminar, organised together with Georgetown University in Washington DC, is "Communicating the Word: Revelation, Translation and Interpretation in Christianity and Islam".
Relations between the Catholic and Anglican Churches have been strained over the past decade over the issue of women priests and homosexual bishops in the Anglican Church, which both leaders have acknowledged as obstacles to unity.