The police could be seen just inside the mosque, removing furniture that the protesters had used as barricades in order to close the door. A police spokesman, Micky Rosenfeld, said that the police had used stun grenades but denied that they had gone deeply into the mosque.

Jordan was already incensed that Israel had closed the site to all worshipers one day last week for the first time in years. Israel said it had taken the step to prevent more violence after an Israeli counterterrorism unit killed a Palestinian suspected in an assassination attempt against a prominent American-born Israeli activist, Yehuda Glick, a leader of the movement challenging the ban on Jewish prayer inside the compound. (Israel, which is in charge of security there, has banned non-Muslim prayer for years to avoid provocations.)

Supporters of Mr. Glick, who was severely wounded in the assassination attempt, had called for Jews to pray for his recovery at the holy site on Wednesday.

Mohammad al-Momani, the Jordanian government spokesman, said Israel must maintain the status quo and not allow “extremists” into the compound to “practice religious practices that are provocative to Muslims.” Hanan Ashrawi, a member of the Palestine Liberation Organization’s executive committee, said Israel was “inciting a holy war in Palestine and throughout the region, with global ramifications.”

The Palestinian ambassador to the United Nations said the Palestinian Authority had written to the Security Council to request that it take action on the tensions at the mosque.

Prime Minister Benjamin Netanyahu of Israel, who says it is the Palestinian leadership that is inciting the violence, has repeatedly said he will not allow any change to the status quo at the site — neither allowing Jews to pray there nor preventing them from visiting.

Israel seized the compound from Jordan in the 1967 war along with the rest of East Jerusalem and the West Bank. Israel then annexed East Jerusalem in a move that was never internationally recognized. Tensions over East Jerusalem, which the Palestinians claim as the capital of a future independent state, rose again last week when Mr. Netanyahu announced that Israel would fast-track planning for 1,060 new apartments in populous Jewish neighborhoods there.