The army said the militants were killed Saturday morning and carried RPG launchers and assault rifles. But it is also Tisha B'av, the day when Jews commemorate the destruction of the first and second Temples on the same site.
Israeli police and Palestinian worshipers clashed at a flash-point Jerusalem holy site on Sunday as overlapping Jewish and Muslim holidays led to tensions there.
The Muslim celebrations coincided with the Jewish holiday of Tisha B'av, which sees an increase in Jewish visits to the Al-Aqsa compound.
"International justice is one-eyed and the justice that is not won through worldwide laws will be taken through the resilience and resistance of the peoples", Bassil went on to say.
Israeli police fired sound grenades to disperse Palestinians during confrontations on Sunday outside Jerusalem's al-Aqsa mosque where tens of thousands of Muslim worshippers gathered for the Eid al-Adha holiday, witnesses said.
It is yet to be decided whether Jewish worshippers will be allowed into the compound, which is the flashpoint of the Israeli-Palestinian conflict.
Israeli Prime Minister Benjamin Netanyahu praised intelligence and security forces for locating and arresting the suspects. It also includes Church of the Holy Sepulchre, one of the most sacred Christian sites in the world. Jewish extremists have called for destroying the mosque and rebuilding the Biblical temple.
Israeli-Palestinian tensions have spiked following President Donald Trump's decision in 2017 to recognize Jerusalem as Israel's capital and move the U.S. Embassy there.
In a separate incident on Sunday, Israeli troops killed a Palestinian gunman after he opened fire on them from across the perimeter fence around the Gaza Strip.
The Palestinian ministry identified the deceased as Marwan Nasser.
"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.
Early in August, Israeli troops shot and killed a Palestinian terrorist who opened fire at forces behind the fence.
No Palestinian group claimed responsibility.