The protesters, mainly students, regathered soon and pelted stones at the police officers and many of the protesters also succeeded to storm the high-security Red Zone. The diplomatic enclave includes several western embassies, including the US, British and French.
The film, titled Innocence of Muslims, has triggered protests in several countries in Africa and Asia, including India, and over 30 people have been killed in violence.
Pakistan saw several instances of protest over the past week and at least two people had been killed. But Thursday was the first time when the protest in the capital became violent.
A protester said the western countries often ridicule Islam and blasphemy is committed against Prophet Mohammad in the name of freedom of speech.
A French satirical magazine published cartoons of the prophet and pictures allegedly demeaning him in its Wednesday edition, which compelled the French government to beef up security at its embassies in several Muslim countries fearing a backlash.