The police used tear gas to disperse the crowd during sporadic clashes through the night outside the embassy, where yesterday thousands of protesters climbed on the embassy walls and tore down the Stars and Stripes. They replaced it with a black Islamic flag.
According to official records, so far 16 protesters have been injured in addition to several police officers.
A police car was also burnt when it attempted to head to the embassy. Police fired tear gas at protesters who were banging stones on metal to make noise. Stones were hurled from both sides.
Protesters chanted a mix of anti-police songs, commonly sung by football fans and the ultras, and religious slogans.
"I am here to defend the prophet and to protest the securitymen who are Muslims and yet preventing me from letting my voice be heard. Nothing has changed under (President Mohamed) Morsi. The revolution will prevail," said protester Abdallah al-Masry, 27, of the Movement of the Revolutionaries of the Egyptian Street.
Morsi has asked the Egyptian Embassy in the US to take action against a blasphemous movie offensive to the prophet of Islam.
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The documentary film had also sparked fury in Libya where four Americans including the ambassador were killed when a mob attacked the US consulate in Benghazi yesterday.
Meanwhile the Muslim Brotherhood called for peaceful protests tomorrow.