Security forces dragged supporters of deposed president Mohamed Morsi from the al-Fath mosque, passing through angry crowds who tried to beat the Islamists, calling them "terrorists".
The clashes came as the government said 173 people had been killed in the past 24 hours alone, bringing the country's death toll to more than 750 since Wednesday, when police cleared two camps of Morsi loyalists in the capital.
According to an AFP tally, at least 1,042 people have been killed since June 26, when Morsi supporters began protesting before mass demonstrations against the Islamist leader that prompted the military to end his single year of turbulent rule on July 3.
The standoff at Al-Fath mosque in central Ramses Square began on Friday, with security forces surrounding the building where Islamists were sheltering and trying to convince them to leave.
The Islamists had lined up the bodies of dozens of protesters who had been killed on Friday inside the mosque-turned-morgue.
By Saturday afternoon, the situation turned violent, with an AFP reporter on the scene saying gunmen inside the mosque were trading fire with police outside.
Police eventually dragged people from inside the mosque, firing in the air to hold back residents of the area who tried to attack the Islamists with sticks and iron bars.
Both outside the mosque and in several other parts of Cairo, residents targeted those suspected of being Islamists, often for no more than wearing a beard or a veil.
On Friday, Morsi supporters had announced "Friday of anger" demonstrations, which quickly turned violent, with gunshots ringing out in Cairo.
The government said those clashes killed at least 173 people across the country, including 95 in the capital and 25 in Alexandria.
Among those killed on Friday was a son of Mohamed Badie, chief of Morsi's Muslim Brotherhood movement.
The Anti-Coup Alliance of Morsi supporters announced it would end the protests shortly after a night-time curfew came into effect, but pledged daily demonstrations going forward.
It was not clear whether that call had been heeded, with no reports of demonstrations in Cairo on Saturday.
The interior ministry said it had arrested 1,004 Brotherhood "elements", and on Saturday security sources said the brother of al-Qaeda chief Ayman al-Zawahiri had been detained.
Security sources also said one soldier was killed in northern Sinai where militants have launched daily attacks against security forces.
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