Israeli security forces entered Jerusalem’s Al Aqsa Mosque compound on Sunday, the last day of the Islamic Eid al Adha holiday.
Al Aqsa, the third holiest site in Islam, is regarded by Jews as the Temple Mount and is considered the most holy place in Judaism.
Palestinians were afraid that Israel would change the rules regarding visitation to the compound, due to Israeli police efforts to allow Jewish activists to tour the courtyards of the mosque.
A police statement said young Palestinians "threw stones and fireworks at police and border police forces."
"These confrontations at the Al Aqsa Mosque come at a very tense time. Over the past several days, there have been frequent confrontations between Israeli security forces and Palestinian worshippers, who go to the site," Al Jazeera's Imtiaz Tyab, reporting from Jerusalem, said.
Defence Minister, Moshe Ya’alon had stated that Muslims were to be allowed to enter the compound without age limitation and Jewish visitors would not be allowed on the compound on Sunday, according to the Times of Israel
Police said the situation was currently "under control."
During the Jewish new year of Rosh Hashana tensions in and around the compound have been running high.