Separately on the Gaza border, a Palestinian shot at Israeli soldiers, who returned fire and killed him in the third such incident in recent days, the army said.
Hamas’ health ministry confirmed the death of the Palestinian.
In Jerusalem, police fired sound grenades as Palestinian protests intensified at the highly sensitive Al Aqsa mosque compound, known to Jews as the Temple Mount.
The Red Crescent reported 61 Palestinians wounded, 15 of whom were taken to hospitals.
Police said four officers were wounded as Palestinian protesters threw stones and other objects at security forces, who responded with what they called riot-dispersal means.
Seven people were arrested, police said.
Yesterday marked the start of Eid Al Adha holiday and thousands of Palestinians prayed at the Al Aqsa mosque.
It coincided with the Jewish Tisha B’av holiday, which typically sees an increase in visits by Jewish religious nationalists to the holy site.
In a bid to ease tensions, police initially barred Jewish visits to the site on Sunday but Muslim worshippers still feared they would be allowed in and protested there. The clashes with police broke out afterward.
After relative calm returned and following criticism from Israeli far-right politicians, police then opened the site to Jewish visits, sparking clashes.
Prime Minister Benjamin Netanyahu said that he decided in advance “in consultation with all the security bodies” to allow Jewish entry.
Palestinian worshippers blocked from entering after the clashes gathered outside and chanted “Allahu Akbar!” and “With my soul and my blood, I will defend Al Aqsa.”
“It’s our mosque, it’s our Eid,” said Assisa Abu Sneineh, 32, adding she was there when the clashes erupted.
“All of a sudden (security forces) arrived and began to hit and fire sound grenades.”
Some 1,300 Jews visited the site yesterday, according to the Muslim Waqf organisation, which administers the holy compound.
Jordan, the site’s custodian and one of only two Arab countries with a peace treaty with Israel, condemned Israel’s “continuous violations” there.
Senior Palestinian official Hanan Ashrawi called Israel’s response “an act of recklessness and aggression.”
The compound, which includes the Al Aqsa mosque and the Dome of the Rock, is one of the most sensitive sites in the Israeli-Palestinian conflict.
It is the third-holiest site in Islam and the most sacred for Jews, who revere it as the location of the two biblical-era temples.
The site is located in east Jerusalem, occupied by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.
Jews can visit but not pray there to avoid provoking tensions.
A potent symbol of Palestinian national identity, it is the scene of regular clashes between Palestinian worshippers and Israeli police.
Yesterday’s incidents come only weeks ahead of Israel’s September 17 elections, and Netanyahu is widely seen as wanting to maintain calm.
The separate incident on the Gaza border followed two similar ones since the start of the month.
On Saturday, Israel’s army said troops shot dead four heavily armed Palestinians on the Gaza border, adding one had managed to cross and throw a grenade at soldiers.
On August 1, a Palestinian seeking to avenge his brother’s death by Israeli fire entered Israel from Gaza and opened fire on soldiers, the army said. Three Israeli soldiers were wounded and the Palestinian was killed, it said.