Youths and activists from political and online groups including the Facebook group "ElBaradei for presidency of 2011" joined the protest. Some chanted "Down Down [Egyptian president] Hosni Mubarak" and "Saeed you are a martyr" while rushing to meet ElBaradei.
Egyptian authorities have said Saeed died after choking while on drugs, denying that torture or violence was the cause of his death.
"Breaking the barrier of fear is an incremental process that takes time. But with democracy we will have no fear"
However, numerous witnesses have reportedly given Human Rights Watch (HRW) corroborating descriptions of Saeed being beaten to death, prompting the rights group on Thursday to call on Egypt to prosecute the culprits.
Amr el-Shobky, a political analyst, said: "We know the price Egyptian citizens pay for giving testimony against the interior ministry or the police force. Yet despite that, those who saw what happened spoke of it."
Saeed's death has become a rallying point for government opponents demanding an end to 30 years of emergency law, which they say allows police to abuse citizens with impunity.
"This gathering of people from all walks of life and the anger they expressed against practices of torture is a message to the regime that Egyptians are against such inhumane practices," ElBaradei told Reuters.
"Breaking the barrier of fear is an incremental process that takes time. But with democracy we will have no fear," ElBaradei said.
Pent up frustration
Thousands of riot police spread across the city and surrounded the mosque, forming a tight cordon around the protesters, but only after ElBaradei was allowed to leave the area.
Earlier protests in Cairo, the capital of Egypt, against police brutality have been forcibly broken up by police and dozens of protesters detained.
ElBaradei visited the neighbouring city of Fayoum in June in a signature drive campaign that drew some 3,500 supporters.
The events in part reflect pent up frustration in Egypt after almost three decades of rule by Hosni Mubarak, the Egyptian president, and with an emergency law that gives authorities wide powers to quash dissent.
Mubarak has no designated successor and has not said if he will seek another term in the 2011 presidential election. If he does not, the most common view is that he will hand power to his politician son Gamal, 46.
ElBaradei, a Nobel peace prize winner, has said he may run in the 2011 presidential vote if there were constitutional reforms, but the existing rules make it almost impossible for an independent to get on the ballot.