An airport official who spoke on condition of anonymity because he was not authorized to speak to the press said Yitzhak Levanon returned to Cairo on a Turkish Airlines flight through Istanbul.
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Playing down the significance of Levanon's trip, a Foreign Ministry official, who asked not to be identified, said the ambassador went to Egypt on Saturday for farewell meetings with foreign and Egyptian diplomats before his retirement.
The Israeli official said the new ambassador to Cairo, Yaakov Amitai, was expected to travel to the Egyptian capital in December to present his credentials, but the embassy would not be staffed or resume normal activity until acceptable security arrangements were in place.
Egyptian rioters ransacked the Israeli Embassy following the killing of six Egyptian soldiers in Sinai as Israel pursued Palestinian militants who infiltrated Israel from Egypt's Sinai desert.
Several Israeli security delegations have visited Egypt during the past two months to discuss the return of the ambassador and to decide on a new embassy location.
Many Egyptians view Israel, which signed a peace treaty with Egypt in 1979 after four wars between the two countries, with hostility. Anti-Israeli sentiment, muted before President Hosni Mubarak was overthrown in February, has become more vocal.
The Associated Press and Reuters contributed to this report