The protesters on Monday burned the Israeli flag and shouted "Expulsion of the ambassador is a national duty."
They also demanded the cancellation of the peace agreement with Tel Aviv.
Jordanian media sources reported that police tried to disperse the protesters using batons, and that three demonstrators have been arrested so far.
Raed Alaa el-Deen Za'eiter, 38, was a Palestinian-born Jordanian citizen who was on his way to meet with family members in the West Bank city of Shechem, when he was shot to death by an Israeli soldier.
The shooting was strongly condemned by the Jordanian parliament. Jordanian Foreign Minister Nasser Judeh told the Israeli ambassador that the kingdom expects the Israeli report to include precise details of the incident.
BA/BA