A group of protesters had holed up inside the the Al-Aqsa mosque compound, known to Jews as Temple Mount, overnight.
The protesters threw rocks, concrete blocks and fireworks at police, but police managed to open the site for Jewish visitors.
Nearby, more Palestinian protesters gathered and police used tear gas and stun grenades to disperse them.
The compound in Jerusalem's Old City is a frequent flashpoint and its fate is a core issue at the heart of the Israeli-Palestinian conflict.
The compound often becomes the centre of tensions on major Jewish holidays such as Rosh Hashana, the Jewish new year, which ends on Tuesday night.