At least 100 Palestinians on the Temple Mount were refusing to leave the area on Sunday afternoon, despite an Israeli decision made on Sunday morning to shut down the site due to security concerns.
The Palestinian Authority and the Waqf instructed the men to arrive at the site on Saturday night and stay put, fearing what they termed a "Jewish takeover."
Approximately 150 Arabs hurled rocks and bottles at security forces in the Old City on Sunday morning shortly after the decision to shut down the compound was announced.
Border Police closed off roads around the Old City and dispersed the rioters into the neighborhood of Wadi Joz, where residents briefly joined in the disturbances. RELATEDEast Jerusalem marred by Yom Kippur violenceUS warns citizens: Avoid Old City on SuccotCritical Currents: Shaping a common civil spaceJerusalem united!
Three rioters were arrested and one border policeman was lightly wounded in the clashes.
Police also arrested Kamal Khatib, a top official from the Islamic Movement's northern branch, on suspicion of fanning the riots.
Many of the Arab rioters were believed to have traveled to the capital from the North.
The clashes come two days after the US State Department called on its citizens to avoid the area over Succot.
According to police, access to the area was barred following a call made throughout east Jerusalem to "come and defend" the mount.
Police also detained senior Fatah official Khitam al-Qadar overnight Saturday on suspicion of inciting Muslims to cause disturbances in the Old City by issuing the call.
Palestinians had claimed that police planned to order groups of Jewish settlers to pray within close proximity of mosques.
Qadar served in the past as the Palestinian Authority's minister for Jerusalem affairs after acting as PA Prime Minister Salaam Fayad's adviser on Jerusalem affairs.
Last week, shortly before Yom Kippur, disturbances flared up across east Jerusalem, beginning when 18 policemen and 15 rioters were hurt during clashes on the Temple Mount, and later elsewhere in the Old City.
Police said some 150 Muslim worshipers participated in the disturbance on the Temple Mount, which began when a group of Jewish visitors entered the compound with a police escort.
Abe Selig contributed to this report
