The Vatican said the pope received the Iranians after his weekly public audience, describing Benedict as "particularly satisfied" with the theme of the meeting.
It examined faith and reason in Christianity and Islam. The joint communique did not mention a speech by the pope in Germany in 2006, when he appeared to associate Islam with violence and irrationality. But the issue of violence was raised.
"Neither reason nor faith should be used for violence; unfortunately, both of them have been sometimes misused to perpetrate violence," said the communique.
It called on Christians and Muslims to go beyond tolerance and accept differences, said generalizations should be avoided and urged that religions not be judged on the basis of a single passage in their holy books.
Benedict has sought to placate anger in the Islamic world over his remarks on holy war in the speech in Regensburg University where he once taught, affirming that a quotation from a 14th-century Byzantine emperor was not his personal opinion.
He said the speech was part of an examination of the "relationship between faith and reason."
The talks in Rome this week were the sixth in a series of meetings between the Vatican's Pontifical Council for Interreligious Dialogue and the Islamic Culture and Relations Organization in Tehran.
The next meeting will be held in Tehran within two years, the communique said.
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