The new security measures triggered Palestinian protests who consider Tel Aviv's move as a breach of the years long arrangement on the holy sites.
Over the past week, there have been daily demonstrations and clashes between Israeli forces and Palestinians.
Six Israeli police officers were injured in the rioting, touched off after Israel installed metal detectors at the Temple Mount in response to a July 14 terrorist shooting near the holy site that killed two Israeli police officers.
The clashes came one day after Israeli occupation police said they were barring men under 50 from entering Jerusalem's Old City for Friday prayers.
Another Palestinian aged 18 died in the West Bank village of Abu Dis when a petrol bomb he was planning to throw at Israeli security forces exploded prematurely, according to the ministry.
Israel is ready to make changes to the security measures put in place at the gates of Al Aqsa mosque compound amid rising tension over the issue.
Israel made a decision to install the metal detectors after Arab-Israeli gunmen had shot two police officers dead.
The violence was prompted by Israel's installation of metal detectors at entry points to Al-Aqsa compound in Beit-ul-Muqaddas. Movement of Palestinians from his village was also restricted by Israeli security services.
The demonstration on Saturday was organized by the Palestinian Forum in Britain, who said they sought to attract attention to Israel's aggression in Jerusalem.
It includes the al-Aqsa Mosque, the third-holiest site in Islam, and the Dome of the Rock.
In protest, thousands of worshipers gathered for Friday prayers at various entrances to the sacred compound.
Three Palestinians were reportedly killed Friday in clashes between rioters and police in Jerusalem and the West Bank.
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