Several hundred Muslims prayed outside two different entrances to the site on Monday in protest over controversial Israeli security measures. Palestinians view it as Israel asserting further control over the site.
Muslims on Monday did not enter the third-holiest site in Islam, the Al Aqsa Mosque in Jerusalem, but instead prayed outside in protest after Israeli authorities installed metal detectors at entrances to the compound.
The new security measures were put in place after an alleged attack on two policemen in the compound on Friday.
The compound known as Haram al Sharif, is also known to Jews as the Temple Mount and includes the Dome of the Rock and the Al Aqsa Mosque.
The entire compound is sacred to Muslims, Jews and Christians.
Several hundred Muslims could be seen praying outside two different entrances to the site around midday on Monday.
TRT World spoke to journalist Gregg Carlstorm in Tel Aviv.
There were protests after the prayer, with crowds shouting: "Aqsa mosque, we sacrifice our souls and our blood." Police later sought to move them back.
"We will not break the solidarity of the people," said Jamal Abdallah, a Palestinian who now lives in the US state of Arizona and was planning to visit Al Aqsa, but changed his mind when he was told of the situation.
Authorities in Tel Aviv claim Friday's attack was carried out by three Arab Israelis who had allegedly fled to the compound after the incident.
They were shot dead on sacred grounds by Israeli forces.
Israel took the highly controversial decision of closing the mosque for Friday prayers, triggering anger from Muslims and Jordan, the custodian of the holy mosque.
The site remained closed on Saturday as well while parts of Jerusalem's Old City were also under lockdown.
Israeli authorities said the closure was necessary "to carry out security checks."
The mosque was partially reopened on Sunday, but with metal detectors in place, while security cameras were also being installed in the area.
Al Aqsa officials have refused to enter and have called on worshippers to do the same.
Muslims across the world view the new measures as Israel asserting further control over the site.
Crowds chanted Allahu Akbar or God is Greatest as they gathered near the Lions Gate entrance to Jerusalem's Old City on Sunday.
On Sunday night, skirmishes broke out between Israeli police and worshippers outside the entrance, with the Red Crescent Society reporting that 17 people were injured.
With tensions high, two mosques in the northern Israeli Arab town of Maghar were targeted by Israeli forces overnight, one with a stun grenade and another by gunshots.
Israeli Prime Minister Benjamin Netanyahu took the decision to install the metal detectors and cameras following a meeting with security officials on Saturday.
He also spoke by phone with Jordan's King Abdullah II on Saturday night before leaving on a trip to France and Hungary.
Abdullah condemned the attack, but also called on Netanyahu to reopen the Al Aqsa compound and stressed the need to "avoid any escalation at the site."
Palestinian president Mahmoud Abbas conveyed a similar message to Netanyahu when the two spoke by phone on Friday in the wake of the attack.
Proposals to change security measures at the compound have sparked controversy in the past.
A plan developed in 2015 between Israel and Jordan to install cameras at the site itself fell apart amid disagreement over how they would be operated.
The Haram al Sharif is central to the Israeli-Palestinian conflict.
It is located in east Jerusalem, illegally occupied by Israel in 1967 and later annexed in a move never recognised by the international community.
It is considered as the third holiest site in Islam after the holy mosque in Mecca and the Prophet Muhammad's mosque in Medina.
Israel frees Jerusalem's Grand Mufti
Jerusalem's Grand Mufti, Muhammad Ahmad Hussein, was released after being detained by Israeli police on Friday.
Hussein had criticised the Israeli authorities for closing the Al Aqsa mosque compound to Friday prayers after the attack.
The Grand Mufti confirmed he had been released, but provided no other details.
His son said he was released without any charge after being questioned.