More than 110 people have been injured as Palestinians re-entered the Al Aqsa Mosque in Jerusalem's Old City for the first time in over two weeks.
Israeli authorities had removed all of the contentious security measures including metal detectors and barriers imposed over the last fortnight and given the go-ahead for worshippers to return.
But Bab Hutta, one of the gates, remained closed.
As Palestinians surged forward to enter the site, Israeli security forces fired tear gas and stun grenades.
The restrictions had been put in place following a shootout which left three Palestinians and two Israeli guards dead on July 14.
Palestinians had protested against the measures while Muslim leaders called for a serious of demonstrations which led to an escalation of tension with Israel's security forces.
Nine Palestinians were killed in the clashes, more than 500 others were injured and dozens of people were arrested.
Raed Saleh, a resident of occupied East Jerusalem, told the Al Jazeera that re-entering the compound on their own conditions was a still victory for Palestinians.
"We never saw this kind of win for our people," Saleh said. "People are coming from everywhere just to support us in this occasion."
"The Israeli government will now understand that Palestinians from Jerusalem will not accept everything they [Israelis] will tell them. We control ourselves. No one is controlling us," he added.
Muslim religious leaders and Palestinian Authority President Mahmoud Abbas are calling for prayers to fully resume at the compound.
"We call on Imams to close all mosques in Jerusalem Friday in order for all worshippers to say Friday prayers in Al-Aqsa Mosque only," said Abdel-Azeem Salhab, the head of the body which oversees the city's Muslim holy sites.
The Arab League said Israel's removal of new security measures wasn't effective in solving the long term crisis between Israel and Palestine.
"Israel's withdrawal from its provocative and illegal actions solves the crisis they themselves created," Ahmed Aboul Gheit, the Arab League secretary-general, said at an emergency meeting of Arab foreign ministers.
"Dealing with Islamic sanctities with such imprudence poses a real threat of igniting a religious war because no Muslim in the world accepts tarnishing al-Aqsa or its closure in the face of the worshippers or placing it under Israeli control," Gheit said.