ElBaradei, who had earlier visited Said's family to offer condolences, struggled to move through the crowd as protesters rushed to reach him, some kissing his hands, others patting him on the back.
Hundreds of police and anti-riot forces surrounded the protesters, who represented several political groups including the pro-reform April 6 youth movement and the banned opposition Muslim Brotherhood, as well as prominent activists and opposition politicians, and ordinary citizens.
Protesters held up signs reading: "Our condolences to Freedom" and "Long Live Egypt". Others chanted "Down with (President Hosni) Mubarak".
They demanded the ouster of Interior Minister Habib al-Adly, who they say has failed to bring to justice those accused of torture.
According to witnesses, Said was killed on June 6 when plainclothes policemen dragged him out of an Internet cafe and beat him to death on a busy Alexandria street.
Egypt's interior ministry said he had died from asphyxiation after swallowing a bag of narcotics when approached by officers.
But rights groups have rejected the official account, and Said has since become a symbol for rights activists against police brutality, for which Egypt has been criticised at home and abroad.
Disturbing images of Said's battered and bruised face have appeared on social networking websites, sparking public outcry and condemnation from local and international rights groups.
Opposition members and political activists have argued that the incident is proof that Egypt's decades-old emergency law, which was renewed last month for a further two years, has created a legacy of police impunity.
Several protests have broken out around the country since Said's death, demanding his alleged torturers be brought to justice.
The Alexandria demonstration also marked a powerful comeback for ElBaradei following weeks away from the public eye, amid criticism that his reform campaign had run out of steam.
Rarely are such numbers out in force in Egypt, where police do not tolerate large political gatherings.
"There were thousands of people, and thousands more in the streets near the mosque," said Hassan Nafaa, the coordinator for the National Association for Change set up by ElBaradei to call for political reforms.
"If the protesters had been allowed to move even 500 metres (yards), thousands more would have joined," he told AFP after the protest.
"We gathered today to mourn the loss of Khaled Said and to mourn the fate of this nation," he said.
ElBaradei, 68, has emerged as Egypt's most high-profile reform champion since his retirement from the Vienna-based International Atomic Energy Agency last year.
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