At least 302 Palestinians have been killed by Israeli fire in Gaza or the border area since March 2018, the majority during the demonstrations and clashes.
According to the Israel Police, tens of thousands of Muslim worshipers gathered on the Temple Mount on Sunday morning for Eid al-Adha prayers.
The terror group cancelled this Friday's protest because of the upcoming Muslim holiday of Eid al-Adha.
Palestinian medics said at least 14 people has been wounded, one seriously, in the skirmishes at the site, which Muslims refer to as the al-Aqsa mosque and Jews as the Temple Mount. Police said that four officers sustained minor injuries.
"The decision to capitulate to Arab terrorism and violence at the holiest place for the Jewish people is the root of the loss off deterrence in other areas", said Smotrich.
The clashes came amid heightened tensions between Israel and the Palestinians, just days after an Israeli soldier was killed south of Jerusalem.
The Israeli military says it killed an unspecified number of militants who had crossed the Gaza perimeter fence and threw a grenade at soldiers.
Qudah, the Jordanian spokesman, also said that the Foreign Ministry had sent a letter of protest to Israel regarding "the continued Israeli violations" through diplomatic channels. The confrontation erupted after Muslim and Jewish holidays coincided on Sunday, resulting in a heated conflict over admittance rights.
Pictures posted online showed crowds running away from the police to escape the tear gas and rubber bullets.
Announcers shortly before had called on worshipers through megaphones and loud speakers to remain on the site in order to deny Jewish entry.
Media reported that police employed stun grenades to evacuate the site. Police spokesmen could not be reached for comment.
Israeli Prime Minister Benjamin Netanyahu praised intelligence and security forces for locating and arresting the suspects.
Jews are barred from praying at the compound under a longstanding arrangement between Israel and Muslim authorities.
However, Israeli settlers who regularly enter the compound often perform Jewish prayers on the site.
But in recent years Israeli religious nationalists have stepped up visits to the site to challenge the arrangement.