Unrest at Jerusalem's Temple Mount (also known as Haram esh-Sharif and the Al Aqsa Compound) led Israeli police to shut off access on Tuesday after several weeks of tension at the location.
Palestinians see Israeli restrictions on the areas as an attempt to cut them from the rest of the Al-Aqsa compound, and turn it into a site where Jewish Israelis can pray.
The Jerusalem police commander subsequently ordered the Mount closed to allow for searches to be carried out.
The incident further heightened tensions at the flashpoint site, home to the Al-Aqsa Mosque and gold-topped Dome of the Rock.
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.
Although Palestinians in East Jerusalem, a part of the internationally recognized Palestinian Territory that has been subject to Israeli military occupation since 1967, they are denied their citizenship rights and are instead classified only as "residents" whose permits can be revoked if they move away from the city for more than a few years.
Saif said incidents in Jerusalem was as a result of the silence of the worldwide community before the violation of all global agreements and human rights.
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Palestinian President Mahmoud Abbas denounced the "dangerous Israeli escalation" and warned of "serious repercussions". At least one entrance to Jerusalem's Old City has also been blocked.
According to the agreement, neighborhoods in Old and New Jerusalem will be developed, a large area will be allocated for office space and investment in infrastructure.
Several dozen worshippers gathered just outside the compound for impromptu prayers as Israeli police stood watch.
Worshippers on the mount have staged protests and clashed with police over the site. Last week, Israeli officials traveled to Jordan for meetings, and Jordanian officials have also visited Jerusalem according to Israeli reports. He also called on the global community to join the fight against Israeli authorities.
Israel closed the structure in 2003, claiming it was used by a heritage organization with ties to the Hamas militant group.