The clashes come after weeks of tension over Bab al-Rahmeh and Bab al-Tawbeh, two areas used by Muslims to pray inside Al-Aqsa compound.
Ten suspects were arrested and an investigation into the incident was ongoing, police said.
The Israeli regime tries to make believe that the victim wanted to attack the Israeli military with a knife while no soldier was injured.Meanwhile, Moussa Mohammed Moussa, a 23-year-old Palestinian boy, succumbed to his injuries.
In a Monday interview with Radio 103FM Erdan said that Israel will not allow "another mosque be built on Temple Mount".
There were no reports of violence in the wake of the closure, which was condemned by Palestinian leaders and others.
The statement called on the global community to break its silence and to promote its positions from condemnation throughout leaflets and statements to practical actions by the United Nations resolution.
Israeli police arrest a Muslim worshiper after a Molotov cocktail was thrown at a police post on Jerusalem's Temple Mount on March 12, 2019.
The incident heightened tensions at the site, which is revered by Jews as the Temple Mount and by Muslims as the Noble Sanctuary.
Several dozen worshippers gathered just outside the compound for impromptu prayers as Israeli police stood watch.
Violent altercations have erupted on several occasions over past weeks as thousands of worshipers have forced their way in to the contested area for Friday prayers. Last week, Israeli officials traveled to Jordan for meetings, and Jordanian officials have also visited Jerusalem according to Israeli reports.
Jordan has offered that the site be closed for long-term renovations.
The Palestinian Authority complained of a "dangerous Israeli escalation". The area was closed in 2003 after allegations that the group overseeing the site was linked to terror activity.
Wasfi Kilani, executive director of the Hashemite Fund for the Reconstruction of Al Aqsa and the Dome of Rock, has said that the issue of the Bab Al Rahmah "revealed the intentions of the extremist Jewish organisations and the scheming of the Israeli occupation forces to judaise Jerusalem and its holy sites".
Videos spread online of scuffles between police and Palestinians before the site was cleared, according to AFP.