Egypt has declared a state of alert as protesters remain on the streets of Cairo, following the storming of the Israeli embassy on Friday.
Security forces fired tear gas and drove armoured vehicles at protesters, who responded by throwing stones and petrol bombs. Hundreds were injured.
The protesters broke into the embassy building, entering consular offices and throwing out documents, officials said.
Israel flew its ambassador and nearly all its diplomats back home.
Hundreds of protesters remain near the embassy, burning tyres in the street, chanting slogans against Egypt's military rulers.
Egypt's governing military council is meeting later on Saturday to address the situation, says the BBC's Bethany Bell in Cairo.
Riot police remain on the streets and live gunshots have been heard, our correspondent says, while the air is still thick with tear gas.
Six members of the embassy staff were trapped inside the building during the riot and had to be freed by Egyptian commandos, an Israeli official told the BBC.
He described the unrest as a "serious blow to the fabric of peace" between Israel and Egypt, one of only two Arab countries - along with Jordan - to have made peace with Israel.
Anti-Israel sentiment has been on the rise in Egypt, propelled by the deaths on 18 August of five Egyptian policemen on the Israeli border.
The Egyptian state news agency Mena said 448 people were injured in the clashes overnight into Saturday.
The unrest began after Friday prayers, when thousands converged on Cairo's Tahrir Square to demand faster political reforms following the ousting of former President Hosni Mubarak in February.
From there, hundreds marched on the Israeli embassy. They smashed through a security wall around the building before a group of about 30 broke in and threw documents out of windows.
An Israeli official told the BBC the intruders had entered consular offices, but not the main embassy.
After initially standing by, police moved against the protesters, firing tear gas. Several vehicles were set alight.
Live TV pictures in the early hours of Saturday showed protesters throwing petrol bombs at police vans which drove at a crowd of people to try to scatter them.
Shots were heard in the area but it is not clear who fired them. Protesters also attacked a police station nearby.
An Israeli official said 80 people - embassy staff, including the ambassador, and their families - were flown out overnight to Israel.
The Israeli consul remains in Cairo as acting ambassador.
The BBC's Hamada Abu-Qamar in Cairo says the protesters want the embassy to be shut down.
Peace treaty tested
There have been protests outside the embassy since the deaths on 18 August of five Egyptian policemen on the border with Israel.
Egyptian officials say they were killed as Israeli forces chased suspected militants across the border.
Gunmen had earlier that day attacked Israeli civilian buses near the Red Sea resort of Eilat, killing eight people.
Cairo called the policemen's death "unacceptable". Israel did not admit responsibility, but said the deaths were regretted.
Correspondents say the incident marked a sharp escalation in tensions between Israel and Egypt. Their 30-year-old peace treaty was already being tested after long-time Egyptian leader Hosni Mubarak was forced from office.
Under Mr Mubarak, ties between the two nations had been stable after a history of conflict.
But his removal has sparked fears among Israeli officials that a less amenable government could take charge in Cairo.