One Palestinian was shot dead by Israeli gunfire in the A-Tur neighbourhood of east Jerusalem, according to the Palestinian health ministry.
A second Palestinian was killed by gunfire in east Jerusalem's Ras al-Amud neighbourhood, while a third was shot dead in Abu Dis in the occupied West Bank, the ministry said, without providing details on the circumstances.
Israel's army confirmed it was involved in clashes in Abu Dis.
In anticipation of protests on Friday, Israeli police barred men under 50 from entering Jerusalem's Old City for prayers, while all women were allowed in.
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Police said later in the day that discretion could be applied in the use of the metal detectors instead of forcing everyone to go through them.
But Palestinian and religious leaders were still calling on worshippers not to enter until they were removed.
Crowds gathered outside Jerusalem's Old City found shops closed and streets around Damascus Gate -- the entrance most heavily used by Palestinians -- blocked.
A group of several hundred people, including Muslim leaders, marched towards the Lions Gate entrance to the mosque compound, but police informed them that only men aged 50 or over would be allowed in.
Police later fired stun grenades and tear gas towards protesters outside the Old City, while Palestinians threw stones and other objects at security forces in some areas.
"They turned back everyone who came here to pray but then I told them I was going to the doctor, but they did not let me in," said Ulfat Hamad, 42, who was visiting from the United States.
"I am going to pray here with others," he said outside the walls.
Tensions have risen since police installed the metal detectors in a move Palestinians and other Muslims perceive as a means for Israel to assert further control over the compound containing the revered Al-Aqsa mosque and Dome of the Rock.