Clashes erupted on Thursday between Palestinians protestors and the police in Jerusalem's Old City after thousands of Muslim worshippers gathered around the contested Temple Mount holy site for evening prayers.
Palestinians are angry because metal detectors have been put in place at the entrance of the Al Aqsa Mosque - one of the holiest sites in Islam.
The participants of the worldwide conference in Baku dedicated to the issue of Jerusalem condemned the closure of Al-Aqsa Mosque and the ban on Jumah prayers.
It was not immediately clear if this means the Palestinians are halting their long-standing security coordination with Israel.
Palestinian leader Mahmoud Abbas announced the freezing of all contact between the two sides.
Three Palestinians had been killed in protests in Jerusalem earlier on Friday in clashes with Israeli forcesover entry restrictions at the holy site of Haram al-Sharif, also known as Temple Mount.
Tensions further increased after Israel placed a temporary ban on Muslim men under the age of 50 from entering the holy site on 21 July.
In a Facebook post on Friday, Omar al-Abed said he was avenging what he called Israel's "desecration" of a Jerusalem shrine.
Spokesman for Algerian Minister of Foreign Affairs Abdel Aziz bin Ali al Sherif strongly condemned on Saturday Israel's serious violations against Muslim worshippers in Jerusalem on Friday, calling on the worldwide community to promptly move to put a stop to these "criminal acts".
On Friday the Palestinian Health Ministry said Mohammed Sharaf, 17, and Mohammad Hassan Abu Ghannam, age unknown, died of gunshot wounds in two neighbourhoods of East Jerusalem somewhat away from the epicentre of tension in the walled Old City.
Speculation had been mounting that Israeli Prime Minister Benjamin Netanyahu might order the metal detectors removed before this week's prayers.
Israel made a decision to install the metal detectors at the entry to the shrine on Sunday.
Some held their prayers outside the wall of the Old City and at West Bank military checkpoints instead of at the mosque.