About 500 Palestinians threw rocks and aimed fireworks at Israeli security forces, who responded with stun grenades, tear gas and rubber bullets. No serious injuries reported.
Islamic militants said a suicide bombing in Afghanistan that killed 12 people was revenge for the film, and called for attacks on U.S. diplomats and facilities in North Africa.
"Innocence of Muslims" was made by an Egyptian-born American citizen from Cerritos and posted on YouTube. At least 28 people have died in violence linked to the film in seven countries. U.S. Ambassador Christopher Stevens and three other Americans were killed in a Sept. 11 attack on the embassy in Benghazi, Libya.
Al Qaeda's branch in North Africa threatened to attack U.S. diplomats. In a statement, al Qaeda in the Islamic Maghreb praised the killing of Stevens and called for attacks in Algeria, Tunisia, Morocco and Mauritania. They condemned the United States for "lying to Muslims for more than 10 years, saying its war was against terrorism and not Islam."
While demonstrations have tapered off in nations like Egypt and Tunisia, protests turned violent in Pakistan and Indian-controlled Kashmir, and hundreds of people continued to rally in Indonesia and Thailand.
The government in Bangladesh blocked YouTube to prevent people from seeing the video, while Google blocked access to the video in Libya and Egypt following violence there, and in Indonesia and India because it says the video broke laws in those countries.
The Associated Press contributed to this report.
