The Egyptian-born sheikh died of natural causes Saturday at the age of 78 at a federal medical centre in North Carolina, where he was serving a life sentence on several terrorism-related charges.
More than 2,000 people attended his funeral in Abdel Rahman's home town of El-Gamaleya in the province of Dakhalia northeast of Cairo, an AFP photographer said.
The mosque was bursting with mourners, and some were forced to pray outside.
Abdel Rahman led the militant Gamaa Islamiya group in the North African country before emigrating to the United States.
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He preached a radical brand of Islam and was seen as having inspired the 1993 bombing of New York's World Trade Center, which killed six people and wounded around 1,000.
"We never met you but we're your students," read one banner at the funeral held up by women wearing the niqab face veil.
"We would have loved him to come back while he was still alive so we could kiss his head and feet. But he has returned dead," she said.
"I attended his lectures. He never encouraged violence or terrorism," she added.
His death came after a long battle with diabetes and coronary artery disease, said the US Bureau of Prisons.
In 2012, Egypt's then Islamist president Mohamed Morsi called for Abdel Rahman's transfer to his homeland for "humanitarian reasons," asking for a "prisoner exchange" with the United States.
Morsi's Muslim Brotherhood has bid farewell to Abdel Rahman on Facebook, while Mussa Abu Marzuk, a top official in the Palestinian Hamas Islamist movement, mourned the sheikh on Twitter.
Al-Qaeda's branches in the Arabian Peninsula and North Africa have called for "the most violent of revenges" against "those who oppressed and jailed him" in a joint statement.
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