Jerusalem's top Muslim cleric, Mohammed Hussein, said protests would continue until the metal detectors are removed from the site, which is known to Muslims as the Noble Sanctuary and to Jews as the Temple Mount.
Three Israelis having dinner in their West Bank home were murdered by a 19-year-old Palestinian wielding a knife Friday.
The move angered Palestinian and other Muslims who saw it as Israel asserting further control over the site.
At the conclusion of the Isha evening prayers, clashes erupted again with Israeli forces firing stun grenades at the crowd, Al Jazeera's Harry Fawcett, who was reporting outside al-Aqsa, said. "During that period, Israeli forces have killed more than 255 Palestinians, majority said by Israel to be attackers". The Palestinian Red Crescent said around 450 people were injured in the chaos, largely from rubber bullets and tear gas inhalation.
The site in Jerusalem's Old City that includes the revered Al-Aqsa mosque and Dome of the Rock has been a focal point for Palestinians.
In anticipation of protests on Friday, Israeli police barred men under 50 from entering the Old City in annexed east Jerusalem for prayers, while all women were allowed in. Palestinians, however, argue that the added security upsets the status quo regarding the governorship of Al Aqsa. Thousands of believers refused to ascend the temple mount through the metal detector, spread out prayer mats in the streets and began to pray. Bin said the attacker was wounded and evacuated to hospital.
The Temple Mount, the site where the ancient Jewish Temple once stood, is considered the holiest site in Judaism, and the third holiest site in Islam.
Jordan, which is the ultimate custodian of the holy site, has also been involved in mediation efforts.