A police spokesman told Efe news agency that access to the Temple Mount which is holy for both Jews and Muslims was shut after dozens of young Arabs threw stones and firecrackers at security officers.
The incidents took place before dozens of Jews assembled at the outer gate that gives access to the site in Jerusalem, demanding their right to pray there.
A Jewish ultra-nationalist group had called for prayers Wednesday at the Temple Mount for their leader, Rabbi Yehuda Glick, who was the target of a Palestinian assassination attempt last week and is still in serious condition.
Police officers stormed the site, where the Al-Aqsa Mosque and the Dome of the Rock are located, and dispersed the protesters who locked themselves inside the mosque.
Jerusalem has been the scene over the past month of street battles between Israeli police and young Palestinians.
The current spiral of violence was unleashed in June following the death of three Jewish teenagers in the West Bank town of Hebron, and the subsequent revenge by Israeli extremists who burned a Palestinian teenager to death.
The bloody war in Gaza last summer, successive Israeli decisions to build settlements in occupied East Jerusalem neighbourhoods, several demolitions of Palestinian houses and inflamatory comments by politicians on both sides have raised tensions to their highest levels in years.