Egyptian protesters entered the Israeli Embassy in Cairo on Friday, after tearing down the wall surrounding the building that houses it.
The assault prompted the Israeli ambassador to rush to the airport early Saturday to leave the country.
Yitzhak Levanon, his family and other embassy staff were waiting at Cairo's airport for a military plane to evacuate them.
Egyptian officials say the protesters threw hundreds of documents out of the building on to the crowd outside.
Protesters converged on the embassy Friday, tearing down sections of the graffiti-covered security wall. Egyptian security forces at the scene made no attempt to intervene.
In Washington, President Barack Obama expressed "great concern" about the situation in Cairo and called on Egyptian authorities to protect the Israeli mission.
Since the fall of former leader Hosni Mubarak in February, calls have grown in Egypt for ending the historic 1979 peace treaty with Israel.
Anger escalated last month after Israeli forces responding to a cross-border militant attack mistakenly killed five Egyptian police officers near the border.
Earlier in the day, thousands voiced their displeasure about the slow pace of governmental reform since Mubarak's ouster.
Protesters are trying to put pressure on the Supreme Council of the Armed Forces to provide a concrete timeline for the return to civilian rule in Egypt. They also want to end the practice of military trials for civilians.
Tahrir Square was the center of Egypt's "January 25 Revolution" that led to Mubarak's departure. It has largely been quiet since July, when security forces dispersed a sit-in by protesters.
Mubarak was in court again Thursday, facing charges that he ordered the killing of 850 protesters during the uprising. He is being tried along with former interior minister Habib al-Adly and six other deputies.
Some information for this report was provided by AP and Reuters.