One protestor was lightly wounded by police as 1,500 to 2,000 people tried to storm the court where Mohamed Taha Mohamed Ahmed, editor of Al Wifaq newspaper, was appearing on charges of casting doubt on the parentage of Prophet Mohammad.
"Oh judges of the Sudan, defend the honour of the Prophet," said a banner carried by the outraged crowd as they chanted "death to the apostate."
Ahmed, prominent Islamist journalist and a member of the Muslim Brotherhood movement, had reviewed an old Islamic manuscript written more than 500 years ago, which casts doubt over the parentage of the Muslim Prophet.
The manuscript entitled "The Unknown in the Life of the Prophet" by Maqreezi, a well-known Islamist historian, says that the prophet Mohammed's father was not Abdullah, as Muslims believe.
He also denies the Hashemite roots of the Prophet Mohammed.
Apostates face the death penalty under Islamic Sharia law.
The National Press Council has ordered Wifaq daily to close for three days starting Friday, for carrying an article which was regarded by some as insulting to the Prophet and angered public.