The first forum between Muslim and Catholic officials at the Vatican aim to defuse tensions between the world’s two biggest faiths.
The Pope said “each individual’s… freedom of religion” must be safeguarded, stressing that religious persecution was “unacceptable”.
There was outrage in 2006 when the Pope linked Muslims to violence in the past.
He apologised for those remarks, saying he was quoting a medieval scholar and never meant to make a direct connection.
But it triggered violent protests and prompted leading Muslim scholars to launch an appeal to the Pope for greater theological dialogue, called the Common Word.
That manifesto now has more than 250 signatories.
In remarks on the third and final day of the conference at the Vatican, Pope Benedict said: “Political and religious leaders have the duty of ensuring… each individual’s freedom of conscience and freedom of religion.”