The lecture was followed by protests from thousands of Muslims around the world.
Benedict has used his visit to seek to heal rifts between Islam and Christianity.
Peace and reconciliation
Barnaby Phillips, Al Jazeera's correspondent in Istanbul, said: "Many people in Turkey were upset with the remarks he made in September and he is not going to be able to defuse that completely but he has taken the sting out of it."
"Religions are for peace and reconciliation - they should not be interpreted otherwise"
Pope Benedict XVI
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After a meeting on Tuesday with Ali Bardakoglu, Turkey's leading Muslim cleric, the pope said: "Religions are for peace and reconciliation - they should not be interpreted otherwise."
He said: "The best way forward is via authentic dialogue between Christians and Muslims, based on truth and inspired by a sincere wish to know one another better, respecting differences and recognising what we have in common."
Bardakoglu also gave a speech, echoing the pope's call for more understanding between Islam and Christianity.
Little protest in Ankara
On Sunday, more than 25,000 Turks showed up to an anti-Vatican protest in Istanbul, but on the streets of Ankara most people went about their daily lives, with only a small protest held outside the religious affairs office hours before the pope arrived.
Reverend Federico Lombardi, a spokesman for the Vatican said: "Today we have the sensation he [the pope] is a welcome guest."
Recep Tayyip Erdogan, Turkey's prime minister, reversed his decision not to meet the pope when he arrived in Turkey on Tuesday.
Erdogan delayed his trip to a Nato summit to meet Benedict on the runway.
Oposition parties in the Turkish government have criticised Erdogan over his climbdown.