The clashes came after days of Palestinian protests over an Israeli plan to renovate two contested holy sites in the occupied West Bank.
Police spokesman Micky Rosenfeld said that seven people had been arrested, and that two of his men were hurt, while Palestinian sources said at least 14 people were injured in the confrontations.
Adnan Husseini, an official from Jerusalem's Islamic Supreme Committee, said the Palestinians had thrown shoes at people they believed to be Jewish extremists intending to pray at the site and upset the delicate status quo.
The Palestinians expressed outrage over the incidents, with chief negotiator Saeb Erekat calling for "urgent intervention" from the United States to get Israel to halt its "attacks" on Al-Aqsa and the two West Bank holy sites.
"These absurd Israeli policies are aimed at destroying international efforts and especially the US administration's efforts to restart a serious and genuine peace process," he added.
Hamas slammed what it called a "vile Zionist attack ... which targets the identity of the Palestinian people, its faith, and the identity of the entire Islamic nation."
Jordan's King Abdallah condemned Israel's "aggressions". "The king warned at a meeting with Palestinian President Mahmoud Abbas that Israel's provocative aggressions on Al-Aqsa would have dangerous repercussions," a palace statement said. "The king stressed that Israel's unilateral measures are very provocative and seek to change the identity of Jerusalem, threatening peace efforts in the region."
The statement quoted Abbas as saying: "It's not enough for the international community, including the United States to condemn Israel, the world should stop Israel." Abbas also feared that Israel's move could "ignite a religious war in the region."
The United Arab Emirates denounced "the savage attacks" by "settlers and occupying forces" on the compound, saying it showed Israel's intention to "Judaize the Holy city."
The Al-Aqsa Mosque compound, known as Al-Haram Al-Sharif, is Islam's third-holiest site after the Kaaba in Makkah and the Prophet’s Mosque in Madinah. The site has been bitterly contested for decades between the Muslims and Jews, and the second Palestinian intifada erupted there in September 2000 after a visit by Ariel Sharon, a right-wing politician who went on to become Israel’s prime minister.
The latest disturbance came after days of unrest in the West Bank town of Hebron over an Israeli plan to renovate the Tomb of the Patriarchs there, another ancient site revered by Jews and Muslims. The plan, which also includes Rachel's Tomb in Bethlehem, has infuriated Palestinians and been criticized by the United States as a "provocative" act that could undermine efforts to relaunch Middle East peace talks suspended during the Gaza war more than a year ago.
