Israel says Egyptian commandos plucked six Israelis to safety from their Cairo embassy as protesters stormed the building on Saturday.
An Israeli official says six security officers were trapped in the embassy and there was a real concern for their lives.
Israel had earlier sent a military plane to evacuate its ambassador, Yitzhak Levanon, and about 80 staff and families.
Egypt's interior minister Mansur al-Eissawy declared a state of high alert and the government announced an emergency meeting to deal with the crisis, as police clashed with protesters.
During the violence, in which one person died of a heart attack and more than 400 people were injured, protesters torched police trucks and attacked regional police headquarters.
They tore down the Israeli flag and dumped thousands of diplomatic documents from a balcony.
The United States, which has poured billions of dollars of military aid into Egypt since it made peace with Israel in 1979, voiced concern about the violence.
US president Barack Obama spoke to Israeli prime minister Benjamin Netanyahu on Friday, calling for the protection of the embassy, the White House said in a statement.
The protests started when thousands massed in Tahrir Square to demand reforms and an end to military trials of civilians.
About 1000 people left the square and marched to the Israeli embassy several kilometres away, the BBC reports.
Chanting "Lift your head high, you are an Egyptian," they demolished about half of the security wall outside the mission with sledge-hammers and a hefty metal bar.
The wall, about two metres high, consists of prefabricated cement slabs recently installed around the building that houses the embassy.
A group of about 30 protestors broke in and threw documents out of windows. An Israeli official told the BBC that the intruders had entered consular offices, but not the main embassy.
In the violence that followed, at least two police vehicles were set alight and demonstrators lit fires in the street outside the embassy.
Police used teargas and fired in the air to try to disperse the crowd. 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.
It was the second big eruption of violence at the embassy since five Egyptian border guards were killed in Sinai last month during an Israeli operation against gunmen, prompting Egypt briefly to threaten to withdraw its envoy.
Daily protests have been held at the Israeli embassy since 18 August.
Rather than abandon the Cairo embassy altogether, Israel has left behind the ambassador's deputy as its representative.