Muslims in the West Bank and Occupied East Jerusalem staged protests as Friday prayers were meant to start. They are opposed to Israel's installation of metal detectors at the Al Aqsa Mosque complex.
At least three people have been killed and scores injured as protests erupted on Friday across Jerusalem and the West Bank.
A teenager was killed in clashes in the Occupied East Jerusalem neighbourhood of Ras al Amoud, the Palestinian health ministry said.
It did not specify who was behind the shooting, but a number of other media outlets reported that the 17-year old had been killed by an Israeli settler.
Clashes between Israeli security forces and Palestinians erupted around Jerusalem's Old City on Friday over new security measures at a highly sensitive holy site.
Tear gas and rubber bullets were fired at protesters and there were unconfirmed reports that live ammunition had been used. This could, however, not be independently verified.
Friday's unrest came after Israeli ministers decided not to order the removal of metal detectors erected at entrances to the Haram al Sharif mosque compound, known to Jews as the Temple Mount, following an attack nearby a week ago that killed two policemen.
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.
The ban against men under 50 came after Israeli ministers decided not to order the removal of metal detectors erected at entrances to the Haram al Sharif mosque compound, known to Jews as the Temple Mount, following an attack nearby a week ago that killed two policemen.
"Entry to the Old City and Temple Mount will be limited to men aged 50 and over. Women of all ages will be permitted," the earlier police statement said.
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.
Starting early in the morning, crowds gathered outside Jerusalem's Old City shops and streets around the Damascus Gate, the entrance most heavily used by Palestinians blocked.
A group of several hundred people, including Muslim leaders, marched towards Lions' Gate entrance to the mosque compound, but police informed them that only men over 50 would be allowed.
Crowds began chanting "Allahu Akbar" (God is Greatest) in protest. It was then that the clashes erupted and heavily armed police could be seen chasing the protesters.
It was not immediately clear how many people were injured or how many people were arrested in the clashes with Israeli police. There were unconfirmed reports that live ammunition had also been used.
Israeli Prime Minister Benjamin Netanyahu stressed that the metal detectors were intended to ensure the safety of worshippers and visitors and not an attempt to disturb the fragile status quo under which Jordan is the custodian of the site and Jewish prayer is forbidden.
Palestinians have been refusing to enter the compound in protest at the metal detectors, and hundreds have been holding prayers outside, with clashes occasionally breaking out with Israeli police.
The main weekly prayers on Fridays draw the largest number of worshippers, typically thousands, and speculation had been mounting that Netanyahu might order the metal detectors removed.
But after consultations with security chiefs and members of his security cabinet, Netanyahu decided not to order them removed.
An Israeli official said the security cabinet "has given police the authority to make any decision to ensure free access to holy sites while maintaining security and public order."
"Israel is committed to maintaining the status quo on the Temple Mount and the freedom of access to the holy sites," the official said in a statement.
Police said they had boosted their forces in and around the Old City, with units "mobilised in all areas and neighbourhoods."
"Day of rage"
Israel began reopening it last Sunday, but with metal detectors in place to prevent weapons being smuggled into the compound.
Tensions have risen since then. In the Gaza Strip, Hamas called for a "day of rage" on Friday.
TRT World's Zeina Awad has more.
Ismail Haniyeh, the leader of Hamas, called on Palestinian demonstrators to confront Israeli troops along the enclave's border on Friday.
"Let Friday be a turning point in the battle in the defence of Jerusalem and Al Aqsa," Haniyeh said in a televised speech.
Calls for peace
The controversy has resonated beyond Israel and the Palestinian territories, with Turkey and the UN Middle East envoy expressing concern.
Nickolay Mladenov, the UN special coordinator for Israeli-Palestinian peace talks, called for calm.
On Thursday, Recep Tayyip Erdogan urged Rivlin to swiftly remove the detectors "within the framework of freedom of religion and worship."
"Given the importance that Haram al Sharif carries for the whole Islamic world, the metal detectors put in place by Israel should be removed in the shortest possible time and an end put to the tension," the Turkish president said.
Rivlin told Erdogan that "the steps taken on the Temple Mount were intended to ensure that such acts of terror could not be repeated."
The Haram al Sharif or Temple Mount is central to the Israeli-Palestinian conflict.
It lies in east Jerusalem, seized by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.
It is considered the third-holiest site in Islam and the most sacred for Jews.