They chanted, "Hang the producer and director of the film."
Protesters also spit on and walked on US and Israeli flags during the demonstration, which was organised by an Islamic group called Sri Lanka Thaweed Jamath.
Abdul Razeek, a spokesman for the group, demanded the US ban the film and said the protests would continue until the film is completely removed from YouTube.
He said protesters were "ready to sacrifice our lives for this."