Police have used stun grenades and rubber bullets against the Palestinians, with an Al Jazeera correspondent at the scene reporting: "It doesn't appear as if the clashes went far beyond the gate where police entered, nor are there reports of any injuries."
The security forces entered the holy site after "masked youths hurled stones and fireworks at police," Israeli police said.
The clashes come at a sensitive time - at the end of the Muslim Eid al-Adha holiday and the beginning of the Jewish Succot festival.
Al-Asqa is the third holiest site in Islam, and is also revered by Jews as the Temple Mount and is considered the most sacred place in Judaism.
Israeli Defense Minister Moshe Yaalon stated that there would be no age restrictions on Muslims allowed to visit Al-Asqa, while he added that Jewish visitors would be barred from visiting the site in order to avoid any tensions between the two groups, the Times of Israel reported.
RIGHT NOW occuption forces firing rubber bullets/sound bombs at worshipers inside masjed AlAqsa #AlAqsaUnderAttack pic.twitter.com/gwT0B1DhqZ
— Abbas Sarsour (@iFalasteen) September 27, 2015
However, Palestinians became agitated after Israeli police tried to give Jewish activists the opportunity to tour the grounds of the compound. They feared that Israel maybe trying to reign in on the pledge by Yaalon not to allow Jews to visit the mosque on Sunday.
Comment: Last November, Netanyahu's Housing Minister said the Israel would demolish Al-Aqsa Mosque and build a Jewish Temple in its place. From February of this year: 1,000 Israeli settlers invade al-Aqsa Mosque in January
It looks as though he will follow through with his destruction of this Muslim holy site.