Separately, at least 20 Palestinians were injured by Israeli army gunfire during a protest in the northern Gaza Strip near the Gaza-Israel border.
Since 1993, Palestinians have seen persistent Israeli settlement expansion in the West Bank which triggered two Palestinian intifadas, or uprisings, the second lasting from 2000 to 2005.
Israel occupied East Jerusalem, including the Al Aqsa compound which is considered by Muslims to be the third holiest place in Islam, during the 1967 Middle East War.
The emir of Kuwait, the king of Jordan and the Egyptian foreign minister are among the notables confirmed to attend the Organization of Islamic Cooperation's extraordinary summit in Istanbul on Friday.
Critical of US plans to move the American embassy to Jerusalem, King Salman has pledged to donate $150 for East Jerusalem's Islamic heritage, and $50 million to the UN agency for Palestinian refugees.
Two of the three Turkish citizens arrested at Al-Aqsa mosque on Friday and released on bail by an Israeli court are now to be deported.
Three Turkish citizens were arrested by Israeli police following evening prayers on Friday at Al Aqsa mosque.
Israeli soldiers shot dead a Palestinian man near the Gaza border while dozens of others were wounded on the "Day of Rage." A second person later died of his wounds, a Gaza hospital official said.
The issue of the Al Aqsa Mosque compound in Jerusalem tops the agenda on the Jordanian king's first visit to Ramallah since 2012.
In an extraordinary meeting in Istanbul, member states of the Organisation of Islamic Cooperation accused Israel of "persistent public statements... that incite religious sensitivities, feed tension and incite violence".
Chaotic scenes unfolded as Israeli police used stun grenades to try to control thousands of Muslim worshippers, who surged into Jerusalem's Al Aqsa Mosque after Israel lifted restrictions imposed at the sacred site.
At least 13 Palestinians have been wounded when Israeli police fired tear gas and rubber-coated steel bullets at Muslims outside the Al Aqsa Mosque compound.
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