Hundreds of Palestinians hurled stones at Israeli policemen and Border Guard officers at the Atarot checkpoint northeast of Jerusalem on Friday, police said.
Police fired stun grenades to disperse the crowd. No injuries were reported.
At another checkpoint south of Jerusalem a few dozens of Palestinians, who do not have permits to enter Israel, hurled stones at Israeli
The riots were prompted by a police decision to limit access to Friday's prayers at the al-Aqsa Mosque to males over 40 years of age and holders of Israeli IDs. The decision effectively bans Palestinians from entering the capital to attend prayers in the third week of the Holy Month of Ramadan.
An estimated 175,000 worshipers attended Friday prayers at the Al-Aqsa Mosque.
Large police forces were deployed around the site and inside the Old City to prevent clashes.
United Arab List-Ta'al MK Ahmad Tibi said Friday that Israel is breach basic human rights by preventing thousands of Palestinians from attending prayers at al-Aqsa.
"The international community has to act to lift the ban on Muslims from the territories to visit Jerusalem," he said.