About 200 city police were deployed to ensure security.
Protest leaders criticised the US over the film, while others shouted "Death to America" during the two-hour protest.
Al-Qaeda's branch in North Africa day called for attacks on United States diplomats and an escalation of protests against the video.
In a statement, al-Qaeda in the Land of the Islamic Maghreb praised the killing of Chris Stevens, the US envoy to Libya. The group threatened attacks in Algeria, Tunisia, Morocco and Mauritania, and condemned the US for "lying to Muslims for more than 10 years, saying its war was against terrorism and not Islam".
The group urged Muslims to pull down and burn American flags at embassies, and kill or expel US diplomats. Protests against the film are spreading and turned violent in Pakistan and Kashmir, while hundreds rallied in Indonesia and Thailand yesterday.
Jana Nalee, a Thai Muslim from Bangkok's Lat Phrao area, said he and his Muslim compatriots want the US and the film producer to apologise to Muslims.
"I personally have no grudges against Americans, but I want the US government and the film producer to take responsibility," he said. Mr Jana did not believe protests by Thai Muslims would be violent like in other countries.
National police chief Priewpan Damapong yesterday said he has instructed police to keep a close watch on the situation, particularly in Songkhla's Hat Yai district to prevent people with ill intentions from creating unrest.