The third was named as Mohamed Khalaf, 17, who died of his severe wounds.
The Red Crescent said 390 Palestinians were hurt in the clashes in Jerusalem, most suffering tear gas inhalation, but others injure by live fire and rubber bullets in Jerusalem.
In an additional controversial security measure, Israel restricted entry to the mosque area and Old City on Friday to men aged 50 and over and women.
The area was swarming with a vast police operation, which prevented the access of the worldwide press in points near the complex, such as the Lions’ Gate.
Palestinians have been refusing to enter the Haram al-Sharif compound in annexed east Jerusalem since Sunday, when Israel began installing metal detectors at entrances to the site following an attack that killed two police officers.
Israeli officials said a knife-wielding Palestinian man killed three Israelis and seriously injured another at a West Bank settlement. And police say they’ve blocked buses of Muslims coming to Jerusalem from around the country.
Palestinian President Mahmoud Abbas said he would freeze all contacts with Israel in protest over the new measures, though it wasn’t clear whether that would target security coordination in the West Bank.
Police in Jerusalem said Friday that it had information of “extremist elements to violate the law” and was stepping up security around the city.
There have been daily confrontations since the installation of the detectors at the entrance to the shrine following a deadly Palestinian attack there last week.
Israeli Prime Minister Benjamin Netanyahu had called for security forces to remove the metal detectors in an effort to diffuse the situation, The Guardian says.
The Arab League condemned Israel s use of “excessive violence” against Palestinians in clashes on Friday outside a highly sensitive Jerusalem holy site, while Egypt called on Israel to exercise reason. It was also the site of an ancient Jewish temple, the holiest place in Judaism.
Friday prayers normally draw thousands of worshippers there.
Since Israel captured the old city it has remained committed to that formula.