The protests broke out when Muslims emerged from mosques following the weekly Friday main prayers to voice their anger at the film made in the United States, which ridicules the Prophet Mohammed and belittles the religion he founded.
In Khartoum, guards on the roof of the US embassy fired warning shots as a security perimeter was breached by dozens of Islamic flag-waving protesters, part of a crowd of thousands who had earlier stormed the British embassy and set fire to the German mission, an Agence France-Presse reporter said.
A police vehicle near the embassy was also torched as hundreds of demonstrators broke through an outer security cordon after one protester was hit by a police vehicle and killed.
Police had earlier fired volleys of tear gas in a bid to prevent the 10,000-strong crowd marching on the US embassy after they had swarmed over the German mission, attacking its facade and tearing down the flag to replace it with a black Islamist one before torching the building.
Violence also erupted in the northern Lebanese city of Tripoli, where a crowd of 300 Islamists attacked and set fire to a KFC restaurant, sparking clashes with police in which one person died and 25 were injured, sources said.
The attack on the US fast-food chain's outlet came as Pope Benedict XVI arrived in Lebanon for a three-day visit, calling for Christian-Muslim coexistence and attacking religious extremism.
With tempers boiling across the Muslim world over the movie since the US ambassador to Libya was killed in an attack on an American consulate in Benghazi on Tuesday, the Pentagon said it has sent a team of Marines to Yemen.
The announcement came as tension spiralled again in Yemen's capital Sanaa, with security forces firing warning shots and water cannon to disperse crowds of protesters trying to reach the US embassy.
Yemeni security forces blocked all roads to the mission, after similar confrontations left four people dead on Thursday.
With much of the anger directed at the US, where the film was made reportedly by 55-year-old Coptic Christian Nakoula Basseley Nakoula and promoted by a rightwing pastor, Washington had earlier ordered security boosted at its embassies worldwide.
In Cairo, where the first protests broke out on Tuesday, protesters again clashed with police outside the US embassy, although calm returned later after the Muslim Brotherhood withdrew a call for nationwide demonstrations, saying it wanted to avoid loss of life and damage to property.
Its about-turn came after Egyptian President Mohamed Morsi said during a visit to Rome on Friday the film was an "aggression" on Islam that distracts from the real problems of the Middle East.
In Iran, meanwhile, thousands of people yelling "Death to America" and "Death to Israel" rallied in central Tehran.
State television showed the crowd streaming out after Friday prayers at Tehran University in which a hardline cleric, Ayatollah Ahmad Janati, blamed the US for the crude film, "Innocence of Muslims," in which actors have strong American accents, which portrays Muslims as immoral and gratuitously violent.
"It is a wonder how those running a country claiming to be a superpower become so stupid in taking such actions," he said.
"In their recent lunacy, they have made a movie - whose finances are said to be paid by the Zionists - to insult the prophet."
In Tunis, police fired tear gas and warning shots as more than 1000 stone-throwing protesters gathered outside the US embassy.
A thick black plume of smoke was seen rising from the embassy car park, with a policeman telling AFP some demonstrators had thrown petrol bombs.
Protests have spread across the Middle East and further afield, including to Bangladesh, Indonesia, Malaysia, Kashmir, Pakistan, Iraq, Israel and the Gaza Strip and Kuwait.
Violence also erupted in Asia, with police saying 86 people were arrested after attacking the US consulate in the Indian city of Chennai.
In Kabul, hundreds of Afghan protesters took to the streets, setting fire to an effigy of US President Barack Obama.
