Israeli troops fired tear gas, stun grenades and deployed a water cannon to disperse stone-throwing Palestinian youths.
Several Israeli police officers were injured after fire bombs were thrown at them.
Emergency services said one officer was shot in the arm as well.
Friday's clashes follow days of unrest at Jerusalem's hilltop compound known to the Muslims as the Noble Sanctuary and to Jews as the Temple Mount.
Thousands of officers have been put on patrol on Friday, and police have banned Muslim men under the age of 40 from praying at the site in an attempt to curb violence.