Clashes broke out on Sunday at Jerusalem's Temple Mount, the holiest site in Judaism and also home to the Al Aqsa Mosque, two days after a Palestinian toddler was killed in a firebombing by suspected Jewish extremists.
Police said masked Palestinian youths at the mosque threw stones at security forces while protesters held aloft photographs of the 18-month-old child killed in Friday's arson attack in Samaria.
Israeli media reported that security forces later sought to create a barrier between the stone-throwers and tourists visiting the mosque complex, which has become a hotbed of Islamist extremism.
Calm began to return to holy site in Jerusalem's Old City later in the morning.
A wave of protests and violent riots has swept Judea, Samaria and parts of Jerusalem since Friday's firebombing, which also critically wounded the toddler's four-year-old brother and parents.
There have also been demonstrations by Israelis and calls for a crackdown on extremism.
On Saturday, clashes broke out at Jalazon refugee camp in the West Bank, where the funeral took place for Laith Khaldi, 16, who the army said was shot by soldiers after hurling a Molotov cocktail.
Clashes had also rocked the Temple Mount a week ago when Palestinians were angered over Jews' access to the compound on an annual day of Jewish mourning. Visits are allowed to the complex, but Jewish prayer is prohibited.
Israeli police briefly entered the mosque during those clashes to shut the doors and lock rioters inside.
AFP contributed to this report.