Bennett met with Public Security Minister Omer Bar Lev and Police Commissioner Yaakov Shabtai after police entered the area to stop rocks being thrown from al-Aqsa Mosque.
"The prime minister instructed to allow organized and safe ascendance of Jews to the Mount, while keeping order at the site," the Prime Minister's Office said.
Bennett thanked the police for handling the matter responsibly and protecting Jews’ freedom of worship.
The prime minister also emphasized that “full freedom of worship on the Temple Mount will be maintained for Muslims, as well, who are marking the Day of Arafa and Eid al-Adha this week.
Nearly 1,700 Jews visited the Temple Mount during the permitted hours, after the violent demonstrators were cleared from the area.
Among them was rebel Yamina MK Amichai Chikli, who sang Hatikvah, the Israeli national anthem. Another Yamina MK, Yom Tov Kalfon, visited the holy site as well.
Images circulating on social media showed a small group of Israeli Jews praying at the site, which is against the rules set by the Jordanian Islamic Trust, known as the Wakf, and generally enforced by Israeli police.
The Temple Mount is Judaism’s holiest site, where the two temples stood. Tisha Be’av marks the anniversary of their destruction in 586 BCE and 70 CE.
Jordan sent an official letter of protest against Israeli “violations” on the Temple Mount, including “storming of the holy compound by extremist settlers under Israeli police protection,” Jordanian news agency Petra reported.
Palestinian and other Arab media reports often characterize any Jews visiting the Temple Mount as settlers, and their actions as “storming,” even when labeling videos of people walking in an orderly fashion.
Jordanian Foreign Ministry spokesman Daifallah al-Fayz said: "The Israeli actions against the mosque are rejected and condemned, and represent a violation of the historical and legal status quo, international law, and Israel's obligations as an occupying power in East Jerusalem.”
The Islamist Ra'am (United Arab List) Party said "Muslims have an exclusive right to the al-Aqsa Mosque and no one else has any right over it."
Ra'am warned worshippers in a statement on Sunday against a "large number of settlers who have been storming and violating the sanctity of the blessed Al-Aqsa Mosque since the morning hours."
Hamas warned on Friday that Israel was "playing with fire" by allowing Jews to visit the Temple Mount and march in the Old City, as it does most years.
The terrorist group called on Gazans to "keep their fingers on the trigger" to defend Jerusalem.
The Red Crescent reported that a number of Palestinians were injured in clashes with police. The majority of the injuries were treated on site, according to the organization.
Ayala Ben-Gvir, wife of far-right Otzma Yehudit MK Itamar Ben-Gvir, went to pray at the Temple Mount with hundreds of other Jews, saying that "it is important not only to sit and cry, but to show up and go on the Temple Mount."
"We are not in exile; we must think how to improve and act for sovereignty and Jewish visits to this holy place,” she said. “Whoever controls the Temple Mount controls the Land of Israel in its entirety, and this is how we will work toward control of this holy and important site."