Thousands of Israelis rallied for their annual nationalist flag march, with some chanting “death to Arabs”.
The event regularly stokes Palestinian anger, and last year tensions in the disputed city exploded into war.
About 3,000 police were sent to the event that marks Israel's 1967 military capture of East Jerusalem, home of the Al Aqsa mosque compound.
The rally resulted in the injury of at least 79 Palestinians, according to the Red Crescent, prompting condemnation from across the Arab region and the UN.
The UAE called on Israeli authorities to reduce escalation and “end the state of tension”.
Israel must “exercise maximum restraint to avoid drifting to new levels of instability”, state news agency Wam said.
The Ministry of Foreign Affairs and International Co-operation “reiterated its firm position on the necessity of providing full protection for Al Aqsa Mosque and stopping serious and provocative violations in it.
“Israel must also respect the role of Jordan in overseeing religious endowments in accordance with international law,” Wam said.
Kuwait also condemned the attacks, saying they provoked Muslims. It called on the United Nations to stop the violations.
“These flagrant violations, which provoke Muslims’ feelings and run counter to international law, have repercussions on international (and) regional stability and security, and increase the opportunities for religious-based confrontations,” Kuwait’s Ministry of Foreign Affairs said.
Its statement called on the UN Security Council to take action and to ensure that Israeli forces respect international law.
Kuwait also urged the protection of Palestinians.
Egypt warned about the consequences of violating any agreement on Al Aqsa Mosque that could exacerbate tensions in Palestine.
“Al Aqsa Mosque is a purely Islamic endowment for Muslims and any violations targeting Arabic, Islamic and Christian identity must be stopped,” Ahmed Hafez, spokesman for Egypt's Ministry of Foreign Affairs, said.
He called on the Israeli authorities to act in accordance with international law and “to intervene immediately to stop these provocative practices that inflame the feelings of Muslims”.
Muhammad Al Khalayleh, Jordan’s Minister of Awqaf, Islamic Affairs and Holy Sites, condemned what he said was the Israeli government's failure to stop the nationalists.
“The occupying authority must stop sponsoring Jewish extremism in order to protect, support and organise it, as this behaviour provokes further conflicts that have grave consequences,” he said in a statement.
“The blessed Al Aqsa Mosque and Al Haram Al Qudsi Al Sharif and its area of 144 thousand square metres is a pure right of Muslims,” the statement said.