The Israelis closed the mosque after the shooting of an activist who campaigns for Jews to be able to pray at Al Aqsa, Islam's third most holy site.
It is the first time in 14 years that worshippers have been barred from the compound.
The mosque was shut following the assassination attempt of a far-right Jewish rabbi yesterday.
Sky's Middle East reporter Tom Rayner has been to the scene. He said: "Tyres have been set alight, there [is] a barricade built at the end of the road and there's a thick smell of tear gas in the air...rocks all across the road that have been used to throw at the Israeli security forces."