The Palestinian Red Crescent emergency service said 136 people were wounded in clashes with police there and elsewhere in Jerusalem, including 83 who were hospitalised.
It says most were wounded in the face and eyes by rubber-coated bullets and shrapnel from stun grenades. Israel said six police officers were wounded.
Earlier on Friday, Israeli troops shot and killed two Palestinians and wounded a third after the men opened fire on a base belonging to Israel’s paramilitary Border Police force in the occupied West Bank, the latest in a series of deadly confrontations in recent weeks that has coincided with the Muslim holy month of Ramadan.
Tensions have soared in recent weeks in east Jerusalem, which is claimed by both Israel and the Palestinians.
At the beginning of Ramadan, Israel blocked off a popular gathering spot where Palestinians traditionally socialise at the end of their daylong fast. The move set off two weeks of clashes before Israel lifted the restrictions.
But in recent days, clashes have resumed due to Israel’s threatened eviction of dozens of Palestinians in the Sheikh Jarrah neighbourhood in east Jerusalem, who have been embroiled in a long legal battle with Israeli settlers trying to acquire property in the neighbourhood.
The US said it was “deeply concerned” about the heightened tensions and called on all sides to work to de-escalate them. It also expressed concern about the threatened evictions.
US State Department spokeswoman Jalina Porter told reporters in Washington: “It’s critical to avoid unilateral steps that would exacerbate tensions or take us further away from peace. And that would include evictions, settlement activity, and home demolitions.”
The Al-Aqsa mosque compound is the third holiest site in Islam. The site is also the holiest site for Jews, who refer to it as the Temple Mount and revere it as the spot where the biblical Temples stood.
Israeli police deployed in large numbers as Muslim worshippers were holding evening prayers at the site.
It was unclear what sparked the violence, but videos circulating online showed worshippers throwing chairs, shoes and rocks at police, who fired stun grenades and rubber-coated bullets to disperse them. Smaller clashes broke out elsewhere in Jerusalem.
The Israeli police said protesters hurled stones, fireworks and other objects at them, wounding six officers who required medical treatment.
It said in a statement: “We will respond with a heavy hand to all violent disturbances, riots and attacks on our forces.”
Earlier, some 70,000 worshippers had attended the final Friday prayers of Ramadan at Al-Aqsa, the Islamic endowment that oversees the site said.
Thousands protested afterwards, waving the green flags of the Islamic militant group Hamas and chanting pro-Hamas slogans.
Neighbouring Jordan, which serves as the custodian of Jerusalem’s Muslim holy sites, had earlier warned Israel against further “provocative” steps, while Israel’s archenemy Iran encouraged the violence.
In the attack on Friday morning, Israeli police said three attackers fired on the base near the northern West Bank town of Jenin.
The Border Police and an Israeli soldier returned fire, killing two of the men and wounding the third, who was evacuated to a hospital.
Israelis and Palestinians are bracing for more violence in the coming days.