He added that he was in touch with Jordanian Islamic Waqf in charge of administering the holy site "to pressure the occupation's government" to put an end to the escalation.
Law enforcers said they evacuated the Al-Aqsa mosque compound after a Molotov cocktail damaged a police post.
Tuesday's clash is just a symptom of mounting tensions on the Temple Mount.
Ten suspects were arrested and an investigation into the incident was ongoing, police said.
Police said that officers acted responsibly to deal with security threats, and that they needed to close the Mount to secure the area. The incident took place near a military post in Hebron, a flashpoint city south of Jerusalem.
Saif said incidents in Jerusalem was a result of silence of the worldwide community before the violation of all global agreements and human rights.
However, the left-wing Israeli organisation Ir Amim criticised the reaction as "disproportionately harsh" and warned, "Continued use of excessive force or action deemed to undermine the status quo is extremely likely to ramp up tensions even further".
Police later announced that the site, which Jews call the Temple Mount and Muslims the Noble Sanctuary, would reopen to worshippers and visitors Wednesday morning. Worshipers have forced the area open and entered on several occasions.
He has also called on the global community to intervene, accusing Israeli police and settlers of "consistently violating the sanctity of the mosque and provoking the sentiments of Muslims".
Recent weeks have seen scuffles over a side building at the site known as the Bab Al Rahmah (Gate of Mercy).
Jordan has offered that the site be closed for long-term renovations.
The Israeli authorities, for their part, have yet to comment on the reported disturbances. This disagreement has reportedly stood in the way of a deal.
Israel closed the structure in 2003, claiming it was used by a heritage organization with ties to the Hamas militant group. The Western Wall is the last supporting wall of the Temple Mount, and is the centre for Jewish prayer from around the world.
Baton-wielding police, al-Dibs said, had attacked dozens of Muslim worshippers earlier Tuesday near the Al-Aqsa compound's iconic Dome of the Rock Mosque.