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JERUSALEM — Israel barred all access to a contested sacred site in the Old City for the first time in many years Thursday, a step that a Palestinian spokesman denounced as “a declaration of war” and one that strained Israel’s crucial alliance with neighboring Jordan.

By nightfall, Israel moved to ease the simmering hostility by announcing the site, which Jews call the Temple Mount and Muslims the Noble Sanctuary, would reopen Friday morning. But the authorities said that Muslim men under 50 would be barred from prayers, as they have been frequently in recent weeks, and that Israeli police officers would be out in force. Palestinian leaders called for a mass protest.

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The rare closing came after an Israeli counterterrorism unit killed a Palestinian man suspected of trying the night before to assassinate a leading agitator for increased Jewish access to the site, a cause that has fueled clashes at the site. It also followed months of rising tension and violence across the deeply divided city of Jerusalem, where Israel recently added 1,000 police officers in an effort to ward off what some specialists warn could become a third Palestinian intifada, or uprising.

There is no more sensitive place in Jerusalem than the revered plateau where the ancient Jewish temples once stood — and where some extremists propose erecting a third one — and where thousands of Muslims now worship daily at Al-Aqsa Mosque and the Dome of the Rock.

Jordan’s king is Al-Aqsa’s official custodian, so its fate has implications beyond the Israeli-Palestinian conflict — on Thursday, the Jordanian minister of Islamic affairs called the closing “state terrorism by the Israeli authorities.” In 2000, a visit to the site by the future Israeli prime minister Ariel Sharon, accompanied by 1,000 Israeli police officers, helped ignite the violent second intifada.

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“You are dealing with flammable material — it would be wise not to meddle in the business of holy places,” said Mustafa Abu Sway, dean of Islamic studies at Al Quds University and a member of the Islamic Waqf council, a trust that administers the site. “The average person is very upset. People are angry, and people are sad.”

East Jerusalem has been boiling since the start of summer, when a Palestinian teenager was kidnapped and killed in an apparent revenge attack for the earlier abduction and murder of three Israelis in the occupied West Bank. Some 800 youths have been arrested, accused of throwing stones or Molotov cocktails.

Events escalated further when a Palestinian driver plowed into a group of pedestrians in the northern part of Jerusalem last week, killing a 3-month-old Israeli baby and a young woman, and on Monday when Prime Minister Benjamin Netanyahu pushed forward plans to expand two Jewish neighborhoods considered illegal settlements by most of the world.

Jerusalem’s 300,000 Arabs, the vast majority of whom have permanent residency but not Israeli citizenship, complain of neglect both by City Hall and by the Palestinian leadership in the West Bank, making the situation especially volatile.

“There are three axes that have come together, leading to escalation and the potential danger of a loss of control,” said Udi Dekel, a former Israeli general and peace negotiator, citing the kidnapping, settlement activity and Temple Mount activism, and poverty and discrimination in the city’s Arab neighborhoods.

Nabil Abu Rudeineh, the spokesman for President Mahmoud Abbas of the Palestinian Authority, called the closing “a grave act” that would “add to the tensions and instability and create a dangerous atmosphere.” The Jordanian minister, Hayel Daoud, urged the international community to pressure Israel to lift the ban right away, the latest in a series of unusually harsh criticism by Jordanian leaders, including an extremely rare rebuke by King Abdullah himself.

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On Thursday, Netanyahu condemned the shooting of the Jewish activist, Yehuda Glick, as “an act of terrorism.” He accused his Palestinian counterpart of inciting violence, pointing to a recent speech in which Abbas called on his people to defend the mosque compound from Jewish encroachment “by all means.”

“I have ordered significant reinforcements, so that we can maintain both security in Jerusalem and the status quo in the holy places,” Netanyahu said after an emergency session with his security team.

Led by Glick and a small band of other activists and right-wing politicians, Jewish visits to the Temple Mount have increased over the past several years, along with protests of the Israeli police’s prohibition of non-Muslim prayer at the site. Some 8,500 Jews ascended the mount last year, up from about 5,800 in 2010, according to the Israel police.

Glick, who has frequently been arrested at the Temple Mount, was in stable but serious condition on Thursday, a hospital spokeswoman said.