The clashes were the latest in a deadly day that saw Israeli forces shoot and kill two Palestinians after three men opened fire on an Israeli base in the occupied West Bank.

They erupted when Israeli police deployed heavily as Muslims were performing evening prayers at Al-Aqsa during the holy month of Ramadan.

Video footage from the scene shows worshippers throwing chairs, shoes and rocks toward the police and officers opening fire.

Israeli police also closed gates leading to Al-Aqsa inside the walled Old City.

Dozens of Palestinians in an east Jerusalem neighbourhood are at risk of being evicted following a long legal battle with Israeli settlers, and Palestinian protesters have clashed with Israeli police in the city on a nightly basis since the start of the Muslim holy month of Ramadan.

The unrest has drawn attention from across the region, with neighbouring Jordan warning Israel against further “provocative” steps, and Iran seizing on the sensitivities around Jerusalem and encouraging the violence.

Israeli police said three attackers fired on the base near the northern West Bank town of Jenin this morning.

The Border Police and an Israeli soldier returned fire, killing two of the men and wounding the third, who was evacuated to a hospital.

Some 70,000 worshippers 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 before dispersing peacefully.

Israelis and Palestinians are bracing for more violence in the coming days.