The injuries occurred when police released tear gas and fired water cannons at the crowd, which had become violent, Antara News reported.
The video, produced in the United States and posted online, has already been blamed for violent outbursts in North Africa and the Middle East.
"The Muslims in Indonesia condemn those who insult Prophet Muhammad. We condemn the American who made the film that insulted Islam," said one of the speakers in the rally.
Vehicles have now been banned from entering the section of central Jakarta where the embassy is located.
Dennis Rodman pledges to end trips to North Korea
Interpol investigating stolen passports on missing flight