Without water and food, and distrustful of the military forces outside the building, those who remained inside said they felt like hostages.
"We want to go home in a very polite way," Amin said. "It's a shame for our military persons to deal with our people like this."
A son of Muslim Brotherhood spiritual leader Mohamed Badie was killed Friday during a protest near the mosque, said the Brotherhood's political wing, the Freedom and Justice party. Ammar Badie, 38, was shot in his neck and head.
Elsewhere in Cairo, the military engaged Friday night in battles with roving bands of armed protesters, state media reported.
Helicopters circled overhead, and there were reports that protesters were trying to shoot them down. Smoke wafted through Ramses Square from a fire that engulfed a nearby commercial building. It was unclear what caused the fire.
Death counts continued to rise in the confrontation that began Wednesday when an estimated 580 people were killed and 4,000 wounded as the military forced pro-Morsy protesters out of encampments in Cairo.
There was no apparent progress toward a political resolution to the crisis. An umbrella group for opponents of the military government called for daily demonstrations next week.
The casualties have not been limited to Morsy supporters and security forces. A number of bystanders, residents and journalists have been killed.
In northern Egypt, at least 25 people were killed and 171 wounded in fighting Friday between Morsy supporters and the military in the coastal city of Alexandria, a government spokesman said Saturday.
The Interior Ministry said 1,004 Muslim Brotherhood members were arrested Friday across Egypt. State-run Nile TV reported Brotherhood members were charged with rioting and creating violence. Authorities seized seven hand grenades, five automatic weapons, pistols and 710 rounds of ammunition, state media said.
French President Francois Hollande and German Chancellor Angela Merkel called for a meeting next week of European Union foreign ministers to coordinate a response.
U.S. President Barack Obama condemned the crackdown by security forces Thursday and canceled scheduled joint exercises by the U.S. and Egyptian military.
Obama received a briefing on Egypt on Saturday, a senior administration official told CNN.
Obama has declined to label Morsy's ouster by the military a coup, a declaration that would stop U.S. military aid to Egypt.