Pope Francis told the Moderator of the General Assembly, the Right Rev Dr Derek Browning, that the Catholic Church andChurch of Scotland enjoy a relationship of "mutual understanding, trust and cooperation."
The two men met for the first time at the Vatican in Rome on Thursday, during the year that marks the 500th anniversary of the Reformation.
Dr Browning presented the Pope with a Church of Scotland Guild tartan scarf, a basket of Scottish produce and a special edition of a book about the history of St Columba and Iona Abbey.
Addressing the Moderator, Pope Francis said: "Let us thank the Lord for the great gift of being able to live this year in true fraternity, no longer as adversaries, after long centuries of estrangement and conflict.
"This has been possible, with God's grace, by the ecumenical journey that has enabled us to grow in mutual understanding, trust and cooperation.
"The mutual purification of memory is one of the most significant fruits of this common journey.
"The past cannot be changed, yet today we at last see one another as God sees us."
Pope Francis, who also received Rev Dr George Whyte, principal clerk to the General Assembly, Rev Dr John McPake, the Church's ecumenical officer and the Moderator's chaplain, Anne Mulligan DCS, said all Christians were brothers and sisters.
Dr Browning told the Pope that the Church of Scotland wanted both denominations to work together for the common good, particularly in the face of national and international anxiety expressed in Sectarianism, anti-Semitism and Islamophobia.
Addressing the Pope, the Moderator said: "If we are in a position of privilege, it is better to build a longer table than a higher fence.
"My Church seeks to ensure that the ministry of our Church continues to reach out to every area of Scotland's life, and to reaffirm that the strength of our Church is to be found at the local, parish level."
Dr Browning said the first thing he noticed was the warmth of the Pope's smile, the strength of his handshake and the intelligence and concern in his eyes.
He said: "The Pope talked about his deep concerns for the people of Myanmar in south east Asia, and especially the Rohingya people and the persecution that many are living with today.
"He has a particular concern for all refugees and asylum seekers, and was interested to hear about the work of Mediterranean Hope, a charity which works with refugees in Italy who have come from the Middle East and Africa."
Dr Browning and his colleagues were given a private tour of the Sistine Chapel, private apartments in the Vatican, and St Peter's Basilica.
On Thursday evening, the Moderator had a private dinner with Justin Welby, the Archbishop of Canterbury, who was also in Rome.
Over the course of the last few days, the Scottish delegation also met with Sally Axworthy, the British Ambassador to the Holy See, Father Dan Fitzpatrick, rector of the Scots College and Rev Luca Maria Negro, president of the Federation of ProtestantChurches in Italy.
