The violence was the latest in days of the worst such disturbances in Jerusalem since 2017, fuelled by a long-running bid by Jewish settlers to take over nearby Palestinian homes in Sheikh Jarrah.
More than 215 Palestinians have been hurt, including 153 who were hospitalised after Israeli security forces stormed Islam’s third holiest site, Al Aqsa Mosque compound.
Israeli security forces fired stun grenades to disperse thousands of Palestinians gathered in in the courtyard of the Al Aqsa compound after morning prayers.
Many Palestinians stayed in the compound following the prayers to keep watch in order to prevent a possible raid by hardline Israeli nationalists.
Tensions have remained high after hardline Israeli nationalists arrived the compound to mark what they call "Jerusalem Day" , the day East Jerusalem was occupied during the 1967 Arab-Israeli war.
Tensions have also been fuelled by the planned evictions of several Palestinian families from the Sheikh Jarrah neighbourhood in East Jerusalem.
Israel's attorney-general secured a deferment on Sunday of a Supreme Court hearing on Monday in the long-running evictions case that had threatened to stoke more violence.