The crowd clashed with the police throughout the night outside the embassy, where thousands of protesters yesterday climbed on the embassy walls and tore down the Stars and Stripes and replaced it with a black Islamic flag.
Police fired tear gas at protesters banging stones on metal to make noise. Stones were hurled from both sides.
The Health Ministry said 70 people were injured in the clashes and 23 people were detained, state media reported.
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.
Meanwhile, President Mohammad Mursi slammed the film but warned against the use of violence.
"We Egyptians reject any kind of assault or insult against our prophet. I condemn and oppose all who... Insult our prophet," Morsi said.
"(But) it is our duty to protect our guests and visitors from abroad," said the president, who is on a visit to Brussels.
"I call on everyone to take that into consideration, not to violate Egyptian law... Not to assault embassies," he added.
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.
