Arab rioters threw rocks and bottles at police at the entrance to the Temple Mount on Friday, when Muslim visitors hold regular prayer services on the holiest site to Judaism.
Police forces dispersed the rioters Friday morning, arresting two of the youths.
There were no casualties in the incident, as prayers on the Mount had already ended.
While riots at the Mount have become common over the past several years, tensions against Israeli security forces have also been rising as the IDF continues to search for the three yeshiva students, who Prime Minister Binyamin Netanyahu confirmed were kidnapped by Hamas terrorists last Thursday night.
Several attacks have been launched against IDF soldiers in the past several days; on Wednesday, Palestinian Arabs in a passing vehicle attempted to run over IDF soldiers stationed near Bethlehem.
The IDF fired at the vehicle; no injuries or damage on the IDF side were reported.The vehicle's trunk was damaged during the shooting as it fled the scene.
On Sunday, assailants shot at Border Police from a passing vehicle near Har Gilo, located just south of Jerusalem and to the north of Bethlehem in Judea.
The attack took place just outside the tunnels leading from Jerusalem to the Gush Etzion area of Judea, an IDF spokesperson stated. No injuries or damage were reported from the attack.