The Islamic Endowments of Jerusalem confirmed that all al-Aqsa gates are now open with no age restrictions imposed, reported Al Arabiya.
Earlier in the day, Israeli forces permitted only men over the age of 50 and women of all ages during Friday prayer.
A Palestinian attempted to stab Israeli soldiers at a junction near Bethlehem in the occupied West Bank on Friday and was shot dead by security forces, the Israeli army said.
The incident occurred at the Gush Etzion junction near a large bloc of Israeli settlements in the West Bank. No soldiers were reported wounded.
Israeli-Palestinian tensions have been high over the last couple weeks due to a dispute over a sensitive Jerusalem holy site, but it was unclear if there was any link.
The Israeli forces clashed with the Palestinian worshipers in the vicinity of al-Aqsa Mosque after Friday prayers.
Al Arabiya correspondent reported that the Israeli forces attacked worshipers north of Bethlehem.
The Islamic Endowments of Jerusalem announced that over ten thousand worshipers performed Friday prayer inside al-Aqsa mosque.
Israeli police said they would bar men under 50 from Friday prayers at al-Aqsa Mosque after clashes erupted as Palestinians ended a boycott of the compound the previous day.
“Security assessments were made and there are indications that disturbances and demonstrations will take place today,” police said in a statement regarding the Haram al-Sharif compound, or the Noble Sanctuary of Jerusalem.
“Only men over the age of 50 will be permitted and women of all ages are permitted. A number of roads around the Old City will be limited to access and all necessary security measures are being taken to prevent and to respond to any outbreak of violence,” it said.
End of boycott
On Thursday, Palestinians ended a boycott of the site over new Israeli security measures there and entered for the first time in two weeks.
Thousands of worshippers streamed into the site on Thursday afternoon. Clashes between Israeli police and Palestinians erupted soon after, with the Palestinian Red Crescent reporting around 100 people wounded.
Palestinians had decided to end their boycott of the site after Israel removed the new security measures, including metal detectors, installed after an attack nearby killed two policemen on July 14.