Deedat, who died on Monday in the South African city of Durban, suffered a stroke in 1996 and had been bedridden ever since.
His stroke came shortly after a trip to Australia during which he gave one of his most influential lectures, Easter: A Muslim Viewpoint.
A statement from the organisation he founded, the Islamic Propagation Centre International (IPCI), on Monday said: "Early this morning, 8 August 2005 / 2 Rajab 1426, Sheikh Ahmed Hoosen Deedat passed on to meet his Creator.
"Throughout this period, he gracefully persevered under the most difficult personal conditions; however, not forgetting his task as a daee (Islamic worker) and an ambassador of Islam, he continued to inspire, educate, challenge and inform people about the universal message of Islam."
Deedat, known for his work on comparative religion, had published more than 20 books and distributed millions of copies of free literature and pamphlets the world over.
Many of Deedat's publications have been translated into the different languages, according to the IPCI website.
He delivered thousands of lectures and participated in numerous public debates globally.
His career in comparative religion involved him in dialogue with the heads of the Protestant church in America and the late Pope John Paul II.
In the 1980s, Deedat was known for his debates with the Christian Evangelist preacher Jimmy Swaggart. He had been refused entry to France and Nigeria on the grounds his opinions might cause civil unrest.
He was awarded the prestigious King Faisal Award in 1986 for service to Islam.
Deedat was born on 1 July 1918 in the Surat district of India.
He emigrated with his father to South Africa in 1927 and settled in Durban, where he was buried on Monday.