The Palestinian official, accompanied by the head of PA intelligence, Majid Farraj, and head of its preventive security, Ziyad Hab al-Reeh, were denied entry at the Hizma checkpoint east of Jerusalem based on instructions from Israeli PM Benjamin Netanyahu, the PA told Ma'an News Agency.
The envoy had planned to head to Jerusalem in an attempt to examine the current situation and support Palestinians residing in the area.
An Israeli Border Police spokesperson did not immediately respond for comment.
Violent skirmishes between Palestinians and Israeli forces skyrocketed across occupied East Jerusalem as the day progressed Friday after emergency border police were deployed and Palestinians faced restrictions entering the Al-Aqsa Mosque for Friday prayers.
Between 8,000 and 10,000 worshipers were estimated to have attended Friday prayers, with over 20 military checkpoints reported to be blocking the path to the mosque compound.
After Friday prayers Israeli forces fired tear gas, rubber-coated bullets, and sound bombs to disperse worshipers near the Damascus Gate, Silwan, and Ras al-Amud.
Over a dozen Palestinians have been injured throughout occupied East Jerusalem and the West Bank so far Friday, with three Israeli police officers sustaining injuries in Jerusalem.
Earlier in the day the UN Security Council urged calm and restraint in the area, asking both sides to refrain from "provocative actions and rhetoric."
Senior Palestinian officials have expressed concerns in recent weeks that Israel is restricting access to the compound in a bid to establish daily Jewish prayer, despite an agreement forbidding non-Muslim worship at the holy site.