Washington, which has poured billions of dollars of military aid into Egypt since it made peace with Israel in 1979, urged Cairo to protect the mission after protesters hurled embassy documents and the Israeli flag from the windows of the building.
Three people were killed and 1,049 wounded in the clashes that began on Friday and raged on into the early hours of Saturday around the Cairo tower block housing the embassy, the Health Ministry said. Police and soldiers had fired shots in the air and teargas to disperse the crowd, who hurled stones at them.
Egypt's army, under pressure to give power to civilians after taking over from toppled ex-president Hosni Mubarak, must balance public calls for a more assertive policy towards Israel with maintaining ties that bring it cash and top-notch U.S. hardware.
"Egypt witnessed a harsh day that inflicted pain and worry on all Egyptians. It is clear that the behaviour of some threatens the Egyptian revolution," Information Minister Osama Hassan Heikal said in a televised statement.
Egypt would transfer those in custody or "involved in inciting or participating in (Friday's) events to the emergency state security court," the minister said, adding that Cairo would use emergency laws still in place to protect the nation.
Protesters lit tyres in the street and at least two vehicles were set alight near the embassy. Many had come from a demonstration earlier on Friday in central Cairo calling for the army to end emergency law and speed up other reforms.
"Our dignity has been restored," said Mohi Alaa, 24, a protester near the site of the overnight clashes. Bits of concrete and bullet casings were strewn over the street.
"We don't want the Americans' money," he said, showing the greater readiness of many Egyptians to express resentment of Israel and the United States after decades of pragmatic official relations.
Some 500 protesters stayed after dawn and a few threw stones at police, who gradually pushed them away and secured the area around the embassy, located on the upper floors of a residential block overlooking the Nile.
It was the second big eruption of violence at the embassy since five Egyptian border guards were killed last month when Israel repelled cross-border raiders it said were Palestinians. Egypt then briefly threatened to withdraw its envoy to Israel.
Israel has stopped short of apologising, saying it is still investigating the Egyptian deaths, which occurred during an operation against gunmen who had killed eight Israelis.
Israeli ambassador Yitzhak Levanon, staff and family members arrived home on Saturday, but one diplomat stayed in Egypt to maintain the embassy, an Israeli official said.
