Israel Police and Border Guard forces were forced to storm the Temple Mount compound Friday after stones were hurled at the end of afternoon prayers.
Officers dispersed dozens of rioters using crowd dispersal means and isolated them. No injuries have been reported.
Three muslim men involved in the incident were arrested - one for hurling stones; two for suspicion of having incited the violent incident.
Dozens of Muslim youths began to hurl stones at the Moroccans' Gate adjacent to the Western Wall as Friday prayers in the Old City ended. Security forces were forced to enter the compound to put a stop to the violence.
The three were taken into custody for questioning as the rest of the worshippers left the area. Jerusalem Police said more arrests are expected over the weekend.
Unlike previous weeks, police decided not to restrict the entrance of young worshippers to the Temple Mount this week.
Police usually only allow worshippers over the age of 50 to enter the site when there is intelligence suggesting others may try to cause provocations.
The decision to allow youths in this week may have been based on eight months of quiet at the site.