One person died of a heart attack overnight and around 450 people were injured, according to Egypt's health ministry.
Friday’s 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.
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 US President Barack Obama called on Cairo to protect the embassy.
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.
Around 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.
Egypt last month asked for an official apology from Israel following the 18 August killing of five policemen along the border, deaths that triggered huge protests outside the embassy.