The renewed violence at the site came despite Israel temporarily halting Jewish visits, which are seen by the Palestinians as a provocation
Medics said more than 150 Palestinians were wounded.
It's the latest in a series of confrontations between Israeli police and Palestinians that threatened to push the contested city toward wider conflict.
At least 113 Palestinians were injured as Israeli security forces used sound bombs to control crowds of worshippers.
The deadlock in the Israeli-Palestinian peace process appears to be illogical and unsettling as a majority of Israelis and Palestinians realize that coexistence, whether under conditions of enmity or friendship, is a fact that neither side can change short of a catastrophe.
"You think there is a magic wand here, but I disagree," he told his political opponents, who have been pushing for peace talks.
At least 53 Palestinians have been killed in attacks and during anti-Israeli protests in the West Bank and Gaza since Oct. 1. Nine Israelis have been stabbed or shot dead by Palestinians.