Mohammed Saud, famous for his command of Hebrew, was spat at, had plastic chairs hurled at him and was verbally attacked during a visit to the Temple Mount, holy to both Jews and Muslims.
The Foreign Ministry is this week hosting bloggers and journalists from Arab countries with whom Israel does not have diplomatic relations, such as Saudi Arabia and Iraq.
Saud, who is part of the delegation, was also branded a "Zionist" and called "garbage." He was told to "pray in the synagogue, not in Al-Aqsa Mosque."
At one point, one protester tried to physically attack Saud, but he was stopped by others who told him, "Don't touch him, we are still in Al-Aqsa."
The footage of the incident shows that Saud did not appear to have been joined by companions, security guards or police.
On Monday, the delegation was in Jerusalem, where they visited the Temple Mount and the Western Wall.
The delegation is expected to visit the Yad Vashem Holocaust Memorial and the Knesset, as well as meet with officials from the Foreign Ministry and academia and Prime Minister Benjamin Netanyahu.