Small groups of Jewish visitors under heavy police guard walked through the mosque compound, known in Judaism as Temple Mount, as thousands of worshippers gathered for the Passover holiday's special "Priestly Blessing" at the Western Wall below.
The Al-Aqsa compound - sacred to Muslims and Jews - has been at the centre of a security crisis set off last week when Israeli police raided the mosque to dislodge what they said were youths barricaded inside armed with rocks and fireworks.
Footage of the raid, showing police beating worshippers, triggered a furious reaction across the Arab world, sparking rocket attacks on Israel by Palestinian factions that were met with Israeli strikes on sites in Gaza, south Lebanon and Syria.
There were no reports of casualties.
Sayyed Hassan Nasrallah, leader of Lebanon's armed Shi'ite movement Hezbollah, met with Palestinian military chief Ismail Haniyeh in Lebanon, the group said on Sunday, and discussed the Al-Aqsa events.
Israeli security experts have said that Iran-backed Hezbollah likely gave its permission to Islamist Hamas to fire the rockets from Lebanon.
"Our enemies were wrong when they thought that Israel's citizens were not united in support for the IDF (Israel Defence Forces)," Prime Minister Benjamin Netanyahu - who is facing unprecedented protests at home against judicial changes - said in a statement.
In Gaza, Hazem Qassem, a Hamas spokesperson urged "all fronts to unite and confront the escalation by the arrogant (Israeli) occupation."
HOLIDAY CLOSURE
The Israeli military said that in light of the security situation, it would extend a closure on the West Bank and Gaza until April 13, when Passover ends.
On Friday, two Israeli sisters from a settlement in the occupied West Bank were killed when their car came under fire by suspected Palestinian gunmen. Hours later, an Italian tourist was killed when a car driven by a man from an Arab city in Israel ploughed into a group in a shoreline park in Tel Aviv.
The funeral of the two sisters, who had dual Israeli and British nationality, is due to be held later on Sunday.
After a year of escalating Israeli-Palestinian violence, tensions are running especially high as Ramadan and Passover coincide, with a focus on the Al-Aqsa compound in Jerusalem's walled Old City. Clashes there between police and worshippers helped spark a 10-day war Israel-Gaza war in 2021.
As in previous years, the government is expected to ban entry to the compound to non-Muslims for the last 10 days of Ramadan, which is expected to end on April 20 or 21, though far-right Security Minister Itamar Ben-Gvir has called for the ban not to be imposed this year.