Security sources also said 53 police officers were injured during the clashes, seven of them also receiving bullet wounds.
The protests against the US embassy began on Tuesday when several thousand people gathered, with one group replacing the American flag with an Islamic one.
The protests have since become smaller, mainly composed of youths sporadically attempting to breach the security lines and enter the embassy.
The protests again broke out when Muslims emerged from mosques following weekly prayers Friday to voice their anger at a crude film made in the United States by a right-wing Christian group that ridicules the Prophet Mohammed.