Protesters chanted slogans such as “Death to Israel” and “No Zionist embassy on Jordanian soil” during Friday’s protest near the Israeli mission in the Jordanian capital.
On Sunday, an Israeli embassy guard shot dead two Jordanians after one of them allegedly attacked him with a screwdriver.
Israel's Foreign Ministry claimed that the guards had acted in self-defense.
However, Jordanian police said that the security officer shot the Jordanian victim, who worked for a furniture company and was delivering an order, after they got into a brawl.
The security man, along with the rest of the embassy staff, returned to the occupied territories under the protection of diplomatic immunity.
The shooter received a warm welcome from Prime Minister Benjamin Netanyahu, who praised him for what he termed acting "calmly.”
Jordanian Foreign Minister Ayman Safadi denounced Netanyahu’s move as “a disgrace,” saying Israel "tried to portray things as if the ambassador and the suspect were under siege, and that they were liberated and celebrated as heroes coming home.”
Jordan has launched an investigation into the deadly shooting incident and Jordan's attorney general has filed murder charges against the Israeli embassy guard.
On Thursday, Jordan's King Abdullah II urged Israel to put the shooter on trial and said the premier's behavior towards the security guard had been "provocative on all fronts and enrages us, destabilizes security and fuels extremism.”
"We demand that the Israeli Prime Minister abides by his commitment and takes all measures to ensure the trial of the killer, and not handle this like a political show to achieve personal political gains," he pointed out.
During Friday’s demonstration, which saw a heavy police presence, the Jordanian demonstrators called for the expulsion of the Israeli ambassador.
"The main headline of this protest is to move the shameful embassy of the Zionist entity from our capital Amman and at the same time to focus on cancelling the shameful agreement of Wadi Araba,” said protester Abdul Majeed Dandees.
He further noted that the Jordanians will continue anti-Israel demonstrations “because the national dignity is a red line for us and Zionists have to understand this."
Another protester, Ahmed al-Ramahi, said, "The demands today are to close this (Israeli) embassy and to say no for Wadi Araba agreement that did not bring anything for the Jordanian people.”
According to a Jordanian government official, the country would not allow the return of Israel's ambassador until the shooting incident is properly investigated.