Thousands of Muslim worshippers surged into Jerusalem's Al-Aqsa Mosque on Thursday and at least 113 were hurt in scuffles with police after Israel lifted security measures imposed at the sacred site in the face of days of violent protests.

Chaotic scenes unfolded as Israeli police used stun grenades to try to control crowds charging forward when the last gate Muslims use to enter Al-Aqsa was opened after a stand-off lasting several hours.

"We will sacrifice ourselves for Al-Aqsa!" chanted the throng outside Islam's third-holiest shrine. Several young men clambered onto the mosque's roof to affix Palestinian flags, which Israeli police soon confiscated.