On the second day of his three-day trip to overwhelmingly Muslim but officially secular Turkey, Francis toured key religious and historical sites in the city once known as Constantinople.
His visit is seen as a crucial test of Francis's ability to build bridges between faiths amid the rampage by Islamic State (IS) jihadists in Iraq and Syria and concerns over the persecution of Christian minorities in the Middle East.
Visiting the Sultan Ahmet mosque — known abroad as the Blue Mosque and one of the great masterpieces of Ottoman architecture — the leader of the world's Roman Catholics paused for two minutes and clasped his hands in reflection.
His gesture was remarkably similar to that of his predecessor Benedict XVI who visited the mosque on the last papal visit to Turkey in 2006.
The pope closed his eyes, clasped his hands in front of his chest beneath the cross he wears around his neck and bowed his head.
He stood next to Istanbul Mufti Rahmi Yaran, who performed an Islamic prayer known as the dua, with his hands in front and palms facing up.
Like Francis, Benedict had turned towards Mecca in what many at the time saw as a stunning gesture of reconciliation between Islam and Christianity.
A Vatican official described Francis's gesture as a "silent adoration", using a term for religious reverence, making clear he did not perform a prayer.
"It was a beautiful moment of inter-religious dialogue," added Vatican spokesman Federico Lombardi.
He described the atmosphere as more "cordial and serene" than during Benedict's visit, which was shadowed by remarks he had previously made deemed to be anti-Islamic.
"It begins to be normal that a pope comes into a mosque," Lombardi said.
After talks with Turkish President Recep Tayyip Erdogan in Ankara on Friday, the pope called for dialogue between faiths to end the Islamist extremism plaguing the Middle East.
Francis also toured the Hagia Sophia, the great Byzantine church that was turned into a mosque after the conquest of Constantinople by the Ottoman army in 1453 but then became a museum in modern-day Turkey.
Francis then celebrated holy mass at the baroque mid-19th century Catholic Cathedral of the Holy Spirit in Istanbul.
Amid heavy security, the close contact with crowds that have been such a feature of past trips by the charismatic Francis appeared to be absent.
Besides the usual hordes of media, just a light sprinkling of believers and well-wishers waved at the pope from behind police barriers as his motorcade drove through the historic centre of Istanbul.
"I am not Christian but I came here out of curiosity and respect. We all need messages of peace and tolerance," said Selime, 70, a Muslim Turk.
Three police snipers stood on each of the two front minarets of the Hagia Sophia for the pope's tour.
True to his pledges to be a pope who eschews extravagance, the pope was driven in a small car, a Renault Symbol, rather than the bulletproof vehicle offered by the presidential palace.
The pope in the evening held an ecumenical prayer in the Orthodox Church of St. George and a private meeting with Patriarch Bartholomew I, the "first among equals" of the world's estimated 300 million Orthodox believers.
In another highly symbolic gesture, the pope asked Bartholomew to kiss his brow in a blessing and bowed his head to show humility.
Francis and Bartholomew — who enjoy warm relations — are working to narrow the differences between the two Churches that date back to the great schism of 1054 that split the eastern and western Christian Churches.
"I believe the pope came here to bridge the divide between Catholics and Orthodox," said Maria Kiliclioglu, a member of Turkey's tiny Bulgarian Orthodox minority. "We need him among us."
Francis is the just the fourth pope to visit the country after Benedict in 2006, John Paul II in 1979 and Paul VI in 1967.
Turkey's own Christian community is tiny — just 80,000 in a country of some 75 million Muslims — but also extremely mixed, consisting of Armenians, Orthodox, Franco-Levantines, Syriac Orthodox and Chaldeans.