Late on Friday, assailants hurled three small pipe bombs at a Greek Orthodox church in Gaza City. A church official said there was little damage to the church and no injuries.
In the West Bank city of Nablus, Palestinian police guarding a Roman Catholic church exchanged fire with would-be assailants and eventually chased them away, residents said.
Abdel Salam Abu Rob, who lives near the church, said intensive shooting was heard for about 20 minutes. There were no immediate reports of injuries.
Police guards were posted at churches in the West Bank and Gaza last weekend after a spate of attacks.
At Islam's third holiest shrine, the Al Aqsa Mosque compound in Jerusalem, hundreds of worshippers hoisted black flags and banners that read "Conquering Rome is the answer". Protesters chanted "The army of Islam will return".
In Nablus, Hamas supporters took to the streets after prayers, shouting slogans against the pope and waving Hamas flags. Raising their hands to the sky, more than 2,000 protesters chanted: "We put up with hunger, detention and occupation, but we won't put up with the offending the prophet. We sacrifice our lives for you prophet."
They called the pope a "coward and agent of the Americans".
In northern Gaza, more than 1,000 Islamic Jihad supporters shouted in praise of the prophet and waved black flags.
Khader Habib, an Islamic Jihad leader, told the crowd that the pope's comments "indicate that this pope doesn't understand Islam or the prophet".
In Ramallah, hundreds of Hamas supporters marched around the city centre.