Palestinians torched a site revered by Jews in the West Bank in an incident that threatened to further inflame two weeks of deadly unrest, as fresh protests erupted Friday.
Palestinian president Mahmud Abbas, under pressure over recent comments that some have labelled incitement, quickly condemned the fire at Joseph's Tomb, in the northern city of Nablus.
Video showed what looked like an extensive blaze, and the Israeli army called it "a despicable act" of desecration.
UN Secretary-General Ban Ki-moon strongly condemned the arson attack at the opening of an emergency session of the Security Council called to discuss the escalating violence.
The arson came as Palestinians called for a "Friday of revolution" against Israel, and police barred men under 40 from attending the main weekly prayers at the flashpoint Al-Aqsa mosque, seeking to keep young protesters away.
Israeli fire killed two Palestinians and wounded 98 others in clashes along the border in the Gaza Strip.
Another Palestinian died in clashes in Beit Furik near Nablus, while protests also broke out in Bethlehem and Hebron.
Outside the West Bank settlement of Kiryat Arba, a Palestinian disguised as a news photographer stabbed and wounded a soldier before being shot dead.
Israeli security forces have deployed massively in Jerusalem after two weeks of Palestinian attacks in the city and across Israel.
Beginning Sunday, some 300 soldiers will reinforce police, stretched thin by the unrest.
On Thursday, Israeli Prime Minister Benjamin Netanyahu reiterated his willingness to meet Abbas, while accusing him of inciting and encouraging violence.
"It's time that president Abbas stops not only justifying it, but also calling for it," Netanyahu told reporters.
US Secretary of State John Kerry, who plans to travel to the region "in the coming days", also warned the Palestinian leader against incitement.
Abbas has called for peaceful protest, but not explicitly condemned any attacks in the recent wave of unrest until Friday's statement on the holy site.
He said the arson "offends our culture and our religion and our morals", and that the damage would be repaired.
The Palestinian leader has faced heavy criticism over a statement Wednesday in which he claimed a Palestinian youth had been executed.
Israel has released photos and videos which they say show the 13-year-old, accused of taking part in two stabbing attacks, recovering in hospital.
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- 'Burning and desecration' -
Joseph's Tomb, inside a compound in the Palestinian refugee camp of Balata in Nablus, has been the scene of recurring violence between Israelis and Palestinians.
Many Jews believe it to be the final resting place of the biblical patriarch Joseph, while Muslims believe an Islamic cleric, Sheikh Yussef (Joseph) Dawiqat was buried there two centuries ago.
The shrine is under Palestinian control and off-limits to Israelis except on escorted trips organised by the army.
The Israeli military said it would make the repairs to allow visits to continue and "take all measures to bring the perpetrators of this despicable act to justice."
There were warnings that the fire could worsen the unrest.
"Burning Joseph's Tomb is a dangerous attempt to exacerbate an already tense environment," Nickolay Mladenov, UN special coordinator for the Middle East peace process, said on Twitter.
Seven Israelis have been killed and dozens wounded in the violence so far, while 37 Palestinians have died, including alleged attackers, and hundreds more been wounded in clashes.
In the intifadas of 1987-1993 and 2000-2005, thousands of people were killed and many more wounded in near daily violence.
- Stabbings defy security crackdown -
On Wednesday, police began setting up checkpoints in parts of annexed east Jerusalem, including a neighbourhood home to three Palestinians who carried out gun, knife and car-ramming attacks this week.
The move followed a decision by Netanyahu's security cabinet authorising police to seal off or impose a curfew on parts of Jerusalem.
Netanyahu has come under immense pressure to halt the violence.
The attackers seem to be mostly acting on their own, with no mastermind for security forces to pursue.
While the attacks have fanned Israeli anger and fear, online video footage of security forces shooting dead alleged assailants has fed Palestinian anger, with protesters seeing some of the killings as unjustified.
The violence began on October 1, when a suspected cell of the Islamist movement Hamas murdered a Jewish settler couple in the West Bank in front of their children.
Those killings followed repeated clashes at east Jerusalem's Al-Aqsa mosque compound in September between Israeli forces and Palestinian youths.