The following prayer is ascribed to him on the Vatican website:
“May Saint John Baptist protect Islam and all the people of Jordan, and all who partecipated [sic] in this celebration, a memorable celebration. I’m very grateful to all of you.”
source
Perhaps the phrase “Protect Islam” refers to the people of Islam rather than their entire system of faith. St. John Paul 2 was quite clear that Islam has false doctrines:
"Whoever knows the Old and New Testaments, and then reads the Koran, clearly sees the process by which it completely reduces Divine Revelation. It is impossible not to note the movement away from what God said about Himself, first in the Old Testament through the Prophets, and then finally in the New Testament through His Son. In Islam all the richness of God’s self-revelation, which constitutes the heritage of the Old and New Testaments, has definitively been set aside. [Paragraph break.] Some of the most beautiful names in the human language are given to the God of the Koran, but He is ultimately a God outside of the world, a God who is only Majesty, never Emmanuel, God-with-us. Islam is not a religion of redemption. There is no room for the Cross and the Resurrection. … [The] tragedy of redemption is complerely absent. For this reason not only the theology but also the anthropology of Islam is very distant from Christianity. … [But we should still] have a dialogue with followers of the ‘Prophet.’ "
source
I especially note how the word Prophet is put in quotation marks. (He does it again on
page 43.) Mohammed is not a true prophet, he is a “prophet.” (I checked the Italian original, the one written by the pope himself, and the quote marks are in that one too.) To me, that is equivalent to identifying Mohammed as a false prophet, and I think that is an important thing to point out.