Associated Press footage shows police throwing stun grenades to disperse protesters in Ras al-Amud, a neighborhood in the eastern part of the city.
The situation began last Friday when three Palestinians exited the Temple Mount armed with submachine guns, killing a Druze Israeli policeman.
The Palestinians responded by throwing stones at the Israeli side.
Protests are breaking out in the occupied old city of Jerusalem after Israeli authorities introduced metal detectors and turnstiles at the entrance of al-Aqsa mosque.
The esplanade of the Mosques, where the dome of the Rock and the mosque al-Aqsa is located in East Jerusalem, the palestinian side of the city whose annexation by Israel was never recognized by the worldwide community.
The israeli army is preparing for possible confrontations with palestinian demonstrators on Friday in the margins of the great prayer, in the wake of new israeli security measures at the entrances to the esplanade of the Mosques in Jerusalem.
In the past two years, Palestinians have killed 45 Israelis, two visiting Americans and a British tourist in stabbings, shootings and car-ramming attacks.
Thousands of police have been deployed around the compound, home of the al-Aqsa mosque and Dome of the Rock.
The violence erupted over a ban on Muslim men under the age of 50 entering the al Aqsa mosque and the installation of metal detectors.
An Israeli official said the security cabinet "has given police the authority to make any decision to ensure free access to holy sites while maintaining security and public order".
Buses carrying Muslim worshippers were barred entry to the city Friday. Muslim leaders have called for protests, holding a "Day of Rage" on Wednesday.
Israel has defended the controversial move, claiming they are no different from security measures at other holy sites around the world.
Under the status quo - which dates back to the Ottoman period - only Muslims have the right to worship on the plaza, although Jews and people from other faiths can visit.
Speaking to the Guardian outside the Old City's Damascus Gate, Jawad Bibis, 50, said he had crossed four checkpoints to reach the street, where he had finally prayed.
Jerusalem Mufti Muhammad Ahmad Hussein demanded the metal detectors be removed, calling them "Israeli aggression".
"Israel is committed to maintaining the status quo on the Temple Mount and the freedom of access to the holy sites", the official said in a statement.
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