Emerging from a mosque hundreds of meters (yards) away from the embassy, the protesters chant "Death to Israel" and "No Zionist embassy on Jordanian soil", an AFP correspondent says.
Israel's embassy staff have since returned to Israel and Mr Netanyahu embraced the security guard and praised his handling of the situation.
Tensions between the two countries have been running at the fever pitch since Sunday evening, when an Israeli security guard shot and killed two Jordanians in an apartment on embassy grounds.
The Jewish state maintained the guard had diplomatic immunity.
Violent clashes have been raging for several days in Jerusalem following Tel Aviv's decision to install metal detectors at the Temple Mount in the Old City. A second Jordanian, the owner of the building, was hit by gunfire and later died of his injuries.More news: Gujarat floods: 25000 people evacuated as heavy rain lash state
More news: Couple arrested in Utah for administering drugs to their newborn
More news: Deaths at Israeli Embassy in Amman Come as Jerusalem Seethes
The dead Jordanian was killed by a gunshot, while the two wounded people including an Israeli were taken to hospital.
Late Monday, Jordan's Public Security Directorate announced that its investigation determined that the assailant had attacked the Israeli guard, though it claimed there had been an argument first between the teen and the guard over a delay in delivering the furniture.
Prime Minister Benjamin Netanyahu spoke last night with Israeli ambassador to Jordan Einat Schlein and with the security guard. One of the workers stole behind the guard's back and started to stab him with a screwdriver.
Now, relations between the neighboring countries appear to be on the brink of collapse after Jordanian terrorist attacked an Israeli embassy security guard in Amman.
Following the call, Netanyahu held a consultation with his security cabinet to discuss a possible "technological solution" that would replace the metal detectors. Abbas deserves an entire column of his own detailing his irresponsibility in almost every aspect of this drama, including his continuing dissembling over alleged threats to the Temple Mount status quo and his shockingly irresponsible and unsafe invitation to the Tanzim militia to lead mass protests this Friday.
The statement said the building was in the Israeli embassy compound, but the Israeli media reports indicated that the building was not part of the compound.