Dozens of worshippers in protective masks were let into the compound before the first prayers of the day, held on a cool and windy pre-dawn break.
Chanting "God is greatest, we will protect Al-Aqsa with our soul and blood", the group gathered in front of the large wooden doors were welcomed by mosque director Omar al-Kiswani, who thanked them for their patience.
It followed a fraught day in annexed east Jerusalem, where the compound is located.
Israeli police on Saturday shot dead a disabled Palestinian they say they mistakenly thought was armed, prompting furious condemnation from Palestinians in the occupied territories.
The religious site, which houses Al-Aqsa Mosque and the Dome of the Rock, closed its doors in March as part of measures to limit the spread of COVID-19.
Muslims believe the Prophet Mohammed ascended to heaven from here, and the site has often been a flashpoint in the Israeli-Palestinian conflict.
The Jews, refer to it as the Temple Mount and believe it to be the location of two biblical temples - the second of which was destroyed in 70 AD.
On the first day of the Eid holiday, scuffles broke out between Israeli police and Palestinians as worshippers tried to break through barriers to enter the compound.
Known to Muslims as the Haram al-Sharif, the site is under the custodianship of neighbouring Jordan, which controlled the West Bank, including east Jerusalem, up until occupation by Israel in the Six-Day War of 1967.
With the number of COVID-19 cases declining, in recent days both Israel and the Palestinian Authority have eased restrictions.
Israel has reported more than 17,000 cases, including 284 deaths.
Fewer than 500 infections and just three deaths have been confirmed in the occupied West Bank and Gaza, which have a combined population of around five million.
Following the deadly shooting on Saturday, the Palestinian leadership demanded that whoever killed the man be brought before the International Criminal Court.
The incident happened in the alleys of the walled Old City near Lions' Gate, an access point mainly used by Palestinians.
There have been fears that Israeli plans to take advantage of a controversial green light from US President Donald Trump to annex swathes of the West Bank could stoke further violence.
This article has been adapted from its original source (AFP)
