Charles also said "extremism and division" are not inevitable, during a special service at Westminster Abbey which celebrated the contribution believers have made in the region.
Addressing more than 1,000 people on Tuesday evening, he said: "Throughout history, in these lands which are the cradle of faith for Jews, Muslims and Christians, communities of different beliefs have shown that it is possible to live side by side as neighbours and friends.
An estimated 100,000 Christians fled the Nineveh Plains of Iraq in 2014 as Islamic State extremists advanced on the city of Qaraqosh.
Premier has reported how Christian organisations such as Aid to the Church in Need have been helping scores of Iraqi families return to their homes.
Others in attendance at the event on Tuesday included the Archbishop of Canterbury Most Rev Justin Welby - as well as members of the Coptic Orthodox Church Centre, Syriac Catholic Church and Iraqi Chaldean Catholic Church.
The prince added: "Co-existence and understanding are not just possible, therefore; they are confirmed by hundreds of years of shared experience.
"Extremism and division are by no means inevitable.
"All three of the great Abrahamic faiths believe in a loving, just and merciful God who cares for creation, who cares for his creatures and who expects us to care for one another."
During recent years, Prince Charles has met many Middle Eastern Christians who now live and worship in the UK.
Concluding the speech, he said: "So in this season of Advent, as we celebrate the birth of our Lord Jesus Christ, who himself knew exile, injustice and suffering, I can only assure you of our steadfast support and most heartfelt prayers as you take forward your works of restoration, justice and healing, so that God's will might be done on earth as it is in heaven."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.