The Pope and his host, the Greek Orthodox leader, Archbishop Christodoulos, issued a joint statement condemning "all recourse to violence, proselytism and fanaticism perpetrated in the name of religion".
Earlier the Pope made a sweeping apology on behalf of Catholics for misdeeds committed over centuries against members of the Orthodox Church.
Rift
The Pope's trip had been preceded by demonstrations by Greek Orthodox hardliners, who refer to the pontiff as "the grotesque, two-horned monster of Rome".
The BBC Athens correspondent, Paul Wood, says it is not clear if the papal statement will be enough for the Greek Orthodox Church.
Achieving the reconciliation so fervently desired by the Pope is no easy task, our correspondent adds.
Before leaving Greece, the Pope led religious services in a covered stadium for the Catholic community in Athens..
Reaching out to Islam
His four-day visit to Syria is going ahead despite troubled times in the region with the collapse of the Middle East peace process.
Syrians are eagerly looking forward to the visit of a world-famous leader, hoping it will improve their country's often negative image.
While in Damascus, he will be the first pope to set foot inside a mosque when he visits the Omayyad mosque, the scene of St Paul's conversion.
The Vatican says it will be the first time that Muslims and Christians have prayed together in an organised way.
The Pope is also due to visit the ghost town of Quneitra on the Golan Heights, which was destroyed by Israeli troops during wars with the Arabs.
Some think it is a rather political move for a religious leader on a spiritual pilgrimage.
Prayer for peace
The Pope will not make a speech there, but will give a personal prayer for peace.
One Western diplomat said the visit would be a good chance to show the Syrian view of the conflict with Israel, something the Pope could perhaps do better than the Syrians themselves.
However, Syria may be more interested in improving its international image by hosting the Pope, than using his visit for political gains on the peace process.
The authorities have been accused of political oppression and sponsoring terrorist groups. But correspondents say there is a high degree of religious tolerance in the country, in a population of diverse faiths and ethnic backgrounds.
The six-day pilgrimage in the steps of the Apostle Paul will also take the Pope to Catholic Malta.