Officials from the Jordanian Islamic Authority had suddenly discovered that the Bab Hutta gate, where two Israel Police officers were murdered by terrorists on July 14, was still closed to the public.
Israel had faced intense pressure over the security devices and said it plans to install sophisticated cameras instead.
Muslims had been refusing to enter the site and prayed in the streets outside for more than a week after Israel installed the new security measures at the compound.
Al-Aqsa Waqf, or pious foundation, a religious trust that manages Islamic buildings at the compound, was hesitant and director Omar Kiswani announced it would not be in a hurry to enter Al-Aqsa.
But as crowds pushed at one of the gates to the compound in the Old City, police fired tear gas and rubber bullets to disperse them, with dozens reported wounded. Injuries came primarily from stun grenades and rubber bullets, the Palestinian Red Crescent said.
Although Israeli authorities have now removed all the barriers and security measures they had put up at Al Aqsa, the incident once again highlights the continuing tensions in Israeli-Palestinian relations.
Earlier in the day, Israeli authorities chose to remove the remaining metal detectors and surveillance cameras at the entrances to the Old City and the Temple Mount in the city of Jerusalem in a bid to ease Arab-Israeli tensions triggered by the recent restrictions. "Netanyahu's comments mark yet another episode of the ongoing vicious attack against al-Jazeera", the statement read, also referring to calls by Saudi-led bloc boycotting Qatar to close the network.
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Israel's removal of the security measures, including metal detectors and CCTV cameras, marked a significant climbdown by Prime Minister Benjamin Netanyahu.
In light of what is happening in Jerusalem, Abbas said the leadership will continue to discuss the situation because it is not over yet. "We must examine and examine other issues". Under the delicate arrangements that have governed the site's administration for decades, Jordan maintains a custodian role, reaffirmed in its peace treaty with Israel in 1994.
"We will wait for the technical committee, which we assigned, to complete its investigation at Al-Aqsa".
Israeli law permits the death penalty, but it has only been used once - the execution of Nazi war criminal Adolf Eichmann in 1962.
The source said that the leadership also made a decision to accelerate the steps to prepare for a meeting of the Central Council of Palestine Liberation Organization and intensify efforts towards reconciliation to end the internal division since mid-2007. "Every so often we see Palestinians running, trying to avoid the heavy-handed dispersal tactics that the Israelis [are using]".
"All installations outside the gates have been removed, which is a victory to our people", Atheem Salhab said.