This incident came weeks after the UNESCO said that the Temple Mount site, on which the Al-Aqsa Mosque is situated, was an integral part of Palestine.
He added that Israeli forces chased Palestinian worshippers and beat them with batons, shut the doors of the al-Qibli Chapel, and fired rubber bullets as well as tear gas canisters to scatter the people who were protesting the desecration of the mosque.
However, for the past several years, Jewish worshipers and foreign tourists have not been allowed inside the compound during the last ten days of Ramadan, as the days are particularly sacred to Muslims, according to the Director of the Islamic Endowment and Al-Aqsa Mosque affairs Sheikh Azzam al-Khatib.
Huge umbrellas have been set up all around Al Aqsa Mosque, Al Qibli Mosque and Al Marwani Mosque to protect visitors from the sun amid preparations to commemorate the last ten days of Ramadan.
The development came only a day after Sheikh Omar al-Kiswani, the director of al-Aqsa Mosque, said at least 35 Palestinian sustained injuries on Monday when almost 250 Israeli soldiers, escorting a crowd of illegal settlers, stormed the holy site and clashed with worshipers.
He said four "masked Palestinians" were arrested for allegedly disrupting the visit by non-Muslims.
Two groups of around 50 Jewish men were said to have shouted racist and provocative slogans and attempted to pray, although it is forbidden for the Jews to do so at the site.
It is located in east Jerusalem, occupied by Israel in 1967 and later annexed in a move never recognised by the global community.
He said the situation at the flashpoint religious site had been contained after police responded to stone-throwing Palestinian worshippers but that no arrests had been made.
Clashes on the sensitive holy site in the past have sparked wider Palestinian violence in Jerusalem and beyond.
The 10 days, which began yesterday, are the most solemn for Muslims and the period attracts the highest number of worshippers to the site.
Israel occupied East Jerusalem during the 1967 Middle East War.