Israel Radio said on Saturday that the plane carrying Yitzhak Levanon, the ambassador, and about 80 others had landed in Israel, Al Jazeera reports.
It followed a protest on Friday in which the Israeli embassy building was attacked by an Egyptian mob in Cairo on Friday night.
After the mob tore down a cement barrier and penetrated the tower block housing the diplomatic mission, some of the six-member staff on overnight security detail feared for their lives and asked via guards that they pass farewells to their families, Reuters Africa reports.
"All that separated them from the mob, at that point, was one wall. We were very concerned, and so were they," said an aide.
The protesters dumped Hebrew language documents out of the embassy's windows, ABC reports.
Egyptian prime minister Essam Sharaf is holding a crisis cabinet meeting and a state of alert has been declared as protestors remain on the streets, burning tyres and chanting slogans against the governing military council, the Guardian reports.
Police fired shots and tear gas to disperse the crowd. Early on Saturday morning around 500 demonstrators remained near the embassy, which overlooks the Nile, and a few threw stones at police and army vehicles but police gradually secured the area, it reports.
The rampage, in which hundreds were injured, further worsened already deteriorating ties between Israel and post-Mubarak Egypt.
The Israeli ambassador, his family and most of the staff and their dependents — some 80 people — were evacuated out of the country by military aircraft overnight, ABC reports.
Israel's consul for state affairs was left behind, as Israel considers its response to the attack by dozens of protesters on the building that houses its diplomatic mission.
Egyptian commandos had entered the embassy building as it was attacked by protesters to escort six Israeli citizens to safety, AFP reports.
US President Barack Obama earlier called on Egypt to "honour its international obligations" to protect the diplomats and told Benjamin Netanyahu, the Israeli prime minister, that Washington was taking steps to resolve the situation.
Al Jazeera reports:
Hillary Clinton, the US secretary of state, also spoke with Mohamed Kamel Amr, the Egyptian foreign minister, who cut short a trip to Poland.
An Israeli government official who wanted to remain anonymous told the Al Jazeera bureau in Jerusalem that Israel was grateful to Obama and Egyptian government for helping to resolve the situation.
But it said the incident was a blow to Israeli-Egyptian relations and a "serious violation of accepted diplomatic behavior".
"This could have been a real tragedy, We are thankful to all who helped resolve this matter. Over the last few hours there was a real concern for the lives of our people," said the government official.
The Israeli embassy has been a focus for protests in Cairo amid a downturn in relations since Hosni Mubarak, the former Egyptian president, was ousted from power in February.