Egypt declared a state of alert on Saturday after protesters stormed the building housing Israel's embassy and clashed with police, prompting a mass evacuation of the ambassador and other staff.
Israeli Prime Minister Benjamin Netanyahu called the mob attack a "serious incident," while US President Barak Obama asked Egypt to protect the embassy housed in a high-rise building overlooking the Nile.
An Israeli official said Ambassador Yitzhak Levanon, other staff and dependants had all left Egypt but a senior diplomat remained behind.
"We left the deputy ambassador to keep up contact with the Egyptian government," the official told AFP in Jerusalem on condition of anonymity.
He said six embassy staff were plucked to safety by Egyptian commandos.
The attack on the embassy was the worst since Israel established its mission in Egypt after becoming the first Arab country to sign a peace treaty with the Jewish state in 1979. Jordan followed suit in 1994.
The violence is also the worst episode in tense relations between Egypt and Israel since the killing of five Egyptian policemen last month on the border as Israel hunted militants after a deadly attack.
One person died of a heart attack overnight and around 450 people were injured, Egypt's health ministry said.
Protesters demolished a security wall around the mission with sledgehammers, removed the Israeli flag and entered the embassy, grabbing thousands of documents which they dumped to cheering crowds.
They also torched police trucks and attacked regional police headquarters in the Giza district housing the embassy.
Hundreds of soldiers backed by armoured cars rushed to the area after Obama called on Cairo to protect the embassy.
Interior Minister Mansur al-Eissawy declared a state of high alert, cancelling all police leave, while Prime Minister Essam Sharaf called for an emergency cabinet meeting on Saturday.
Quoting an "informed source" government daily Al-Ahram reported on its website that "there is clear intention that the government will submit its resignation after its failure to contain" the violence.
The embassy attack came as about 1,000 protesters marched to the mission from Tahrir Square where thousands had massed to press Egypt's military rulers to keep promises of reform after a January-February revolt ousted president Hosni Mubarak.
Protesters hacked away at a protection wall surrounding the high-rise building housing the embassy while staff were trapped inside.
Israeli Defence Minister Minister Ehud Barak's office said he called US Defence Secretary Leon Panetta early on Saturday to request help protecting their embassy in Cairo's Giza district.
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Obama spoke to Netanyahu by phone and expressed "great concern about the situation at the embassy, and the security of the Israelis serving there," the White House said.
Israel's Ynet news website said Netanyahu thanked Obama.
"The mob attack on the Israeli embassy is a serious incident but could have been worse had the rioters managed to get through the last door and hurt our people," Ynet quoted Netanyahu as saying.
"I'm glad we managed to prevent a disaster and would like to thank US President Barack Obama for his help," he said.
Israeli public radio said the six rescued men were security officers, and Netanyahu's office said they had returned home safe.
The six were "successfully rescued by Egyptian commandos," the Israeli official said in Jerusalem.
"When the violence got out of hand, some 80 (Israelis) were taken out" of Egypt, he added. "All our people are safe and sound."
Some 30 anti-riot police trucks and armoured vehicles were parked on Saturday in the area of the embassy where streets were strewn with rocks and broken glass from the overnight violence, an AFP reporter said.
Some roads leading to the embassy and Giza police station were blocked.
Egyptian state television said that Levanon met a general of the ruling military's Supreme Council of the Armed Forces before leaving Cairo, and that the Israeli ambassador appeared "anxious and even scared."
Protesters played cat-and-mouse with police throughout the night, amid clouds of tear gas and smoke from burning tyres.
They dumped documents in Arabic, English and Hebrew, bearing watermarks of the embassy, to thousands of people on the streets who jostled to grab them like trophies.
The documents ranged from requests to Egyptian authorities for weapons permits for embassy security to internal correspondence about holidays.
A former Israeli ambassador to Egypt, Zvi Mazel, said he believed that the documents were not top secret.
"It may be that our people anticipated something like this and destroyed the most secret things," he told Israeli public radio.
Egypt last month asked for an official apology from Israel following the August 18 killing of five policemen along the border, deaths that triggered huge protests outside the embassy.
Since president Hosni Mubarak's ouster in February, activists have called for a revision of the peace treaty.