The pope's last hours in Istanbul were dedicated to the Catholic community in Turkey. Benedict XVI celebrated mass in the Cathedral of the Holy Spirit in Istanbul.
The mass was also attended by the Orthodox Patriarch Bartholomew I and by faithful of other Christian rites.
Pope Benedict has said that existing divisions among Christians are a scandal. During the service, the pope again said his hope is for full unity to be reached among Christians.
"This hope has not yet realized, but the pope still longs to see it fulfilled," he said.
In words that appeared addressed to Muslims, the pope also said the church wishes to impose nothing on anyone and that it merely asks to live in freedom.
Pope Benedict has made efforts to ease tension with Muslims during his four-day visit to Turkey. He has tried to convince them he is interested in cooperation rather than confrontation.
On Thursday he became the second pope to enter a Muslim place of worship. He visited the Blue Mosque and prayed with an imam while facing Mecca. He told the Muslim cleric that this visit would help them find together the way of peace for the good of humanity.
The pope appeared to have won over Turks with his conciliatory gestures towards Islam and his support for Turkey's EU-bid.
But while in Turkey the pope also called for greater religious freedom for Christian minorities.
Before leaving the Cathedral, the pope thanked Turkey for the cordial way in which he was welcomed everywhere.
The pope expressed deep thanks, saying he was aware that his presence these days has created not few inconveniences to the ordinary life of the people here.
