Clashes also took place at two other West Bank locations - Qalandiya and Kadom. Also in Hebron Palestinians rioted, responding to a call by the Hamas for a "day of rage."
The clashes came amid building tensions in the area, mostly over Israel regime try to change the status quo at East Al-Quds holy site by allowing Jewish to the holy site.
Such a move would break a status quo that has been in effect since Israel occupy the area in the 1967 War.
Israeli politicians have increasingly stirred tensions by visiting the holy site.
Friday for the second week in a row, Al-Aqsa mosque were open to all Muslim worshippers regardless of age. Muslims officials said 45,000 people attended the prayers.
After Israeli authorities dropped age restrictions for attending Friday prayers for the second week running, tens of thousands of people made their way to the Al-Aqsa mosque compound in occupied Arab east Jerusalem.
Weekly Muslim prayers at Al-Aqsa mosque passed peacefully despite tensions in the Holy City, but Palestinians later wounded two Jews as they walked to the holy site.
The Palestinians have been infuriated by a far-right Jewish campaign for prayer rights at the compound that threatens an ultra-sensitive, decades-old status quo under which Jews may visit but not pray.
On Thursday four more demolition notices were issued in east Jerusalem, including to the families of two cousins who carried out an attack on a synagogue on Tuesday.
In recent weeks eleven israeli have been killed by Palestinian in five separate incidents, mostly in Jerusalem, but also in Tel Aviv and the West Bank. The attack were response to Israeli government and Jewish settlers actions in recent weeks.
Five of the Palestinian assailants were martyred by security forces.Hamas praised that attack.
"What happened in Jerusalem is a normal response to the crimes carried out by the Zionist occupation and it is connected to the right to defend Jerusalem as the capital of the Palestinian state and to defend the Al-Aqsa mosque and the holy Muslim and Christian sites," Hamas leader Ismail Haniyeh said Friday.