The moment was "even more meaningful than an apology" for the pope's recent remarks where he appeared to equate Islam with violence, Cagrici said.
In a speech 10 weeks ago the pope quoted a Byzantine emperor who suggested that Islam was an intolerant and violent religion. The speech outraged Muslims around the world.
"It was something beautiful, a gesture on [the Pope's] part ... even more meaningful than an apology"
Mustafa Cagrici, the mufti of Istanbul
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The main purpose of the long-planned trip - seeking reconciliation between the Western and Eastern rites of Christianity - was symbolised by a Saint Andrew's Day mass on Thursday.
However, the trip also focused on healing differences between Christianity and Islam following the pope’s controversial speech.
The visit saw unprecedented security measures. Large areas of Istanbul closed down and the routes taken by the pope's motorcade were kept secret.
Even before the controversy over his remarks on Islam, the pope faced an uphill struggle to win over the Turks, having been considered the "anti-Turkish pope" for opposing Ankara's bid to join the European Union.
He made an U-turn on the issue moments after arriving in Ankara on Tuesday, offering his support for the troubled candidacy in remarks to Recep Tayyip Erdogan, Turkey’s prime minister.
But he added provisos on Thursday. He said respect for religious freedom must be a criterion for entry into the EU, and called on the bloc to ensure that its members respect the rights of their religious minorities.
Pope Benedict also returned to a familiar position when he called for a renewal of "Europe's awareness of its Christian roots, traditions and values".