Israel's ambassador, Yitzhak Levanon, his family and other embassy staff were waiting at Cairo's airport for a military plane to evacuate them, said airport officials who spoke on condition of anonymity because they were not authorized to speak to the media.
Hundreds of protesters converged on the embassy throughout the afternoon and into the night, tearing down large sections of the graffiti-covered security wall outside the 21-story building housing the embassy. Egyptian security forces made no attempt for hours to intervene.
Just before midnight, a group of protesters reached a room on one of the embassy's lower floors at the top of the building and began dumping Hebrew-language documents from the windows, said an Egyptian security official who spoke on condition of anonymity because he was not authorized to speak to the media.
In Jerusalem, an Israeli official confirmed the embassy had been broken into, saying it appeared the group reached a waiting room on the lower floor. He spoke on condition of anonymity because he was not permitted to release the information.
No one answered the phone at the embassy late Friday.
Since the fall of Hosni Mubarak in February, calls have grown in Egypt for ending the historic 1979 peace treaty with Israel, a pact that has never had the support of ordinary Egyptians. Anger increased last month after Israeli forces responding to a cross-border militant attack mistakenly killed five Egyptian police officers near the border.
Several large protests have taken place outside the embassy in recent months without serious incident. Friday's demonstration, however, quickly escalated with crowds pummeling the security wall with sledge hammers and tearing away large sections of the cement and metal barrier, which was recently put up to better protect the site from protests.
For the second time in less than a month, protesters were able to get to the top of the building and pull down the Israeli flag.
Crowds outside the building photographed documents that drifted to the ground and posted some of them online.
Protesters clashed with police and set fire to a police truck outside the embassy. Crowds also tried to attack a nearby police station but were turned back by security forces firing tear gas and warning shots. State radio reported that one person died of a heart attack and that 163 people were injured.
Senior Israeli officials were holding discussions on the embassy breach.
Israeli Defense Minster Ehud Barak said in a statement that he also spoke with his American counterpart, Leon Panetta, and appealed to him to do what he could to protect the embassy.
Thousands elsewhere protested for the first time in a month against the country's military rulers.
Seven months after the popular uprising that drove Mubarak from power, Egyptians are still pressing for a list of changes, including more transparent trials of former regime figures accused of corruption and a clear timetable for parliamentary elections.
Egyptians have grown increasingly distrustful of the Supreme Council of the Armed Forces, which took control of the country when Mubarak was forced out on Feb. 11 after nearly three decades in power. The council, headed by Mubarak's defense minister, Field Marshall Hussein Tantawi, has voiced its support for the revolution and those who called for democracy and justice.
But activists accuse it of remaining too close to Mubarak's regime and practicing similarly repressive policies, including abusing detainees. The trials of thousands of civilians in military courts has also angered activists.
"In the beginning we were with the military because they claimed to be protectors of the revolution, but month after month nothing has changed," said doctor Ghada Nimr, one of those who gathered in Tahrir Square.
One banner in Cairo read, "Egyptians, come out of your homes, Tantawi is Mubarak."
Demonstrators in Cairo also converged on the state TV building, a central courthouse and the Interior Ministry, a hated symbol of abuses by police and security forces under Mubarak. Protesters covered one of the ministry's gates with graffiti and tore off parts of the large ministry seal.
Protests also took place in Alexandria, Suez and several other cities.
About 850 people were killed in the early days of the Jan. 25-Feb. 11 uprising. Tantawi is scheduled to testify in Mubarak's trial in closed sessions that begin Sunday. The 83-year-old Mubarak is on trial on charges of complicity in the deaths of protesters, a charge that could bring the death penalty.
The judge in the trial banned TV cameras from the courtroom during this week's sessions, and starting Sunday the proceedings will be closed to the media and the public.
The lack of transparency in trials of members of Mubarak's inner circle has angered many in Egypt.
"These are all practices of the old regime: repression and restriction on freedoms," said Cairo protester Khaled Abdel-Hamid.