Israeli authorities then closed the compound, citing security concerns, hours before Muslim Friday prayers.
Tensions have soared since Friday.
The spiritual leader of the Al Aqsa Mosque, Sheikh Ikrima Sabri, was injured on Tuesday by a rubber bullet after praying outside the gates of the compound, Palestinian medical personnel confirmed.
The protests follow clashes between Israeli forces and protesters on Tuesday after evening prayers in the occupied city.
"The closure of Al Aqsa Mosque for prayers by Israel is not acceptable".
Hastert released from prison
At the time, Hastert said he was "deeply ashamed" and said, "I know why I am here". "They got him on what they could", he said. The Illinois Republican admitted to sexually abusing underage boys while he worked as a high school teacher and coach.
The Waqf, Jordan's Islamic authority that runs religious affairs of the state and serves as the custodian of the Muslim-administered site, issued a statement on Monday that instructed all Muslims "to reject and boycott all the Israeli aggression measures", the Associated Press reported.
In a statement, Israeli police spokesman Micky Rosenfeld said that Israeli forces removed worshippers at Lions' Gate for allegedly blocking the street while performing prayers.
Fridays in Jerusalem are often a time of heightened security as it's the holy day of the week for Muslims and Shabbat for Jews begins at sundown. It is Islam's third-holiest site after Mecca and Medina in Saudi Arabia.
The security measure was implemented after two Israeli border police officers were killed in an attack at the site on Friday.
When the al-Aqsa compound reopened, metal detectors had been installed, which angered Muslim religious authorities.
They called on the faithful "not to enter the mosque through" the detectors.
"Preserving security and stability in holy places is a Jordanian objective, but this can not be achieved by changing the historic status quo but through respecting it", said Safadi. Despite the fact that the custodianship of the mosque is in the hands of the Jordanian government, Israeli leaders have insisted on the right to install metal detectors.
In the meantime, Abbas is in touch with Arab and worldwide leaders to try to "prevent a deterioration of the situation", it said. Meanwhile, Israeli Prime Minister Benjamin Netanyahu is meeting with Israeli security and defense officials in order to assess the situation in the Old City.