The pope, who has faced calls for an unequivocal apology to the Muslim world but has so far only said he regrets the offence his words caused, said he hoped the furore could lead to "self-critical" dialogue among faiths and cultures.
In a speech in Germany last week, the pope quoted 14th-century Byzantine Emperor Manuel II Palaeologus saying everything Prophet Muhammad brought was evil, "such as his command to spread by the sword the faith he preached".
At his weekly public audience in the Vatican on Wednesday, the German-born pope, speaking in Italian, said once again that the furore was caused by a "misunderstanding".
The pope said: "But for the careful reader of my text it is clear that I in no way wanted to make mine the negative words pronounced by the medieval emperor and their polemical content does not reflect my personal conviction.
"My intention was very different. I wanted to explain that religion and violence do not go together, but religion and reason do."
The 79-year-old leader of the world's one billion Roman Catholics said he hoped the whole furore could eventually serve to encourage "positive and even self-critical dialogue, both among religions as well as between modern reason and the faith of Christians".