He said Israeli soldiers opened fire when the terrorists tried to climb the fence, and that the terrorists returned fire before being killed.
Facing off with police in the packed compound outside Islam's third-holiest site, Palestinians chanted: "With our soul and blood we will redeem you, Aqsa".
But some settler groups have been lobbying Israeli authorities to allow Jewish visitors on the site during Tisha Be' Av, so they can mourn the destruction of a temple believed to have been located there 2,000 years ago.
"The gate was supposed to open at 7:30 but the police is showing weakness and fear, and has not yet announced whether to open the gate to Jewish "visitors" for fear of rioting by "local" Muslims", tweeted Maariv's Avishai Grinzaig.
The Shin Bet security service said Saturday that two suspects have been arrested in the killing of IDF soldier Dvir Sorek in the West Bank, following intelligence and operational activity.
It was not immediately clear what sparked the violence at the site, which Muslims refer to as the Al-Aqsa mosque compound and Jews refer to as the Temple Mount.
It is yet to be decided whether Jewish worshippers will be allowed into the compound, which is the flashpoint of the Israeli-Palestinian conflict. Jewish extremists have called for destroying the mosque and rebuilding the Biblical temple.
It is located in east Jerusalem, occupied by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the global community. Jewish tradition also maintains that Jews should avoid entering the holy site. The Israeli-Palestinian peace process has been moribund for at least a decade, and the Palestinians have cut ties with the Trump administration over what they see as its bias toward Israel.
The Jordanian Foreign Ministry slammed Israel on Sunday for using force against Palestinians at the Al-Aqsa Mosque, the Jerusalem holy site known to Jews as the Temple Mount, after clashes erupted there between the Israel Police and Muslim worshipers earlier in the day.
No Palestinian group claimed responsibility.
"We hold Hamas responsible and accountable for any acts of violence emanating from the Gaza Strip whether they were Hamas operatives or not", he said at a briefing with reporters.
Associated Press writer Fares Akram in Gaza City, Gaza Strip contributed.