The metal detectors were removed early Tuesday morning.
Tensions between Israelis and Palestinians over the site have surged in recent days in response to the metal detectors, which were put in place following the killing nearby of two Israeli policemen. The move incensed the Muslim world and triggered violence. Even the smallest perceived change to delicate arrangements pertaining to the site sparks tensions.
Emerging from a mosque hundreds of metres (yards) away from the embassy, the protesters chanted "Death to Israel" and "No Zionist embassy on Jordanian soil", an AFP correspondent said.
At least one person has been killed and two others injured in a shooting incident at the Israeli embassy complex in Jordan.
The compound is considered the third holiest site in Islam, and the most sacred for the Jewish.
The site, administered by Muslim authorities, is known to Muslims as Haram al-Sharif and to Jews as the Temple Mount, and is home to the al-Aqsa mosque and the Dome of the Rock.
Father of Jordan attacker demands investigation into son's killing
Two Jordanians have been killed and an Israeli wounded in an incident next to Israel's embassy in Amman , BBC News reports. Two Jordanians later died, according to the agency and the news site Hala Akhbar, linked to the Jordanian military.
Israeli Prime Minister Benjamin Netanyahu said Monday he will arrange the return of the guard to Israel. "We will dedicate all the efforts and resources of the Jordanian state to ensure that justice takes its course".
The guard then shot the Jordanian worker and the Jordanian landlord standing next to him, the public security directorate said.
The Jordanian worker was installing furniture at the Israeli embassy compound. The family met in Jordan on Monday and is asking the King of Jordan to act.
Netanyahu told the guard, identified only by his first name, Ziv, that there was never a question about bringing his home. Netanyahu said that he was "happy to see you, and happy that things worked out".
President Abbas has suspended all contacts between the Palestinian Authority and the Israeli government on Friday in protest of the metal detectors. It has always been a flashpoint of anti-Israeli protests at times of turmoil in the Palestinian territories.
Mohamad al Hejouj, a former member of parliament who is related to the Jawawdeh clan, said he was informed by government security officials that Jawawdeh might have "attacked" the security guard.
Israeli media reported that high resolution cameras capable of detecting hidden objects would be deployed. Israel's Ministry of Foreign Affairs and defense officials are working on various channels vis-a-vis the Jordanian government.