Israeli police clashed with masked, Palestinian protesters near al-Aqsa mosque in the Old City of Jerusalem when violence erupted after Friday's Ramadan morning prayers.
Israeli security forces have been on high alert after a series of deadly Arab street attacks throughout the country during the past two weeks, and confrontations at the holy site carry the risk of sparking wider conflict between Israel and Palestinian resistance movements in Gaza.
Tensions have been simmering in Jerusalem, with the Muslim holy month of Ramadan coinciding with the Jewish celebration of Passover and Christianity's Easter festival this year.
Police said they entered the compound, revered by Jews as the Temple Mount and by Muslims as the Noble Sanctuary, to break up a violent crowd that remained at the end of the morning prayers. They did not enter Al-Aqsa mosque - Islam's third-holiest site.
The Palestinian Red Crescent ambulance service said 59 people were injured, some by tear gas and rubber bullets.
Reuters video showed officers, some in riot gear, running after a small number of individuals after most of the crowd had left.
Hamas, which controls Gaza, condemned the Israeli police and said Israel "bears responsibility for the consequences."