Spokeswoman Luba Samri said the suspects were connected to yesterday's riots in which Palestinians barricaded themselves inside a mosque at the site and then threw firebombs and rocks at officers outside during a major Jewish holiday.
The hilltop compound in Jerusalem's Old City is a frequent flashpoint and its fate is a core issue at the heart of the Israeli-Palestinian conflict. It's known to Jews as the Temple Mount, site of the two biblical Jewish temples. Muslims revere it as the Noble Sanctuary, where they believe the Prophet Muhammad ascended to heaven.
Recent violence at the site has raised worldwide fears of widespread unrest.
The site remained quiet today but some violent protests broke out elsewhere. In the West Bank city of Ramallah, about 200 protesters affiliated with president Mahmoud Abbas' Fatah party marched toward an Israeli checkpoint where they attacked troops with rocks. The Israeli forces dispersed the protest with tear gas and rubber bullets, injuring five lightly. Similar clashes took place in Bethlehem as well.