Thousands of worshippers streamed into the Haram al-Sharif compound, known to Jews as the Temple Mount, for afternoon prayers on Thursday, according to witnesses.
The Jerusalem site includes the Al-Aqsa mosque and the Dome of the Rock.
There were initially celebratory scenes as worshippers poured into the holy site with some crying as they entered Islam’s third-holiest site while others shouted "Allahu Akbar" (God is Great).
However clashes between Israeli police and Palestinians erupted shortly after the worshippers entered the site, according to AFP.
The Palestinian Red Crescent reported 46 people wounded both inside the Haram al-Sharif compound and in the immediate area.