Several dozen Palestinians chanted 'God is greatest' as they gathered in alleys of Jerusalem's old city leading to the Western Wall where thousands of Jews were attending the Priestly Blessing during the Jewish festival of Sukkoth, or Feast of Tabernacles, according to Israeli police.
Four Palestinians were reportedly arrested for disrupting order.
Scuffles erupted between Israeli police and other Palestinians who tried to prevent the arrests at the Old City's narrow alleyways. No injuries were reported.
There have been similar days of unrest at al-Aqsa over the past several weeks, which has raised international concern, during a period coinciding with the onset of major Jewish and Muslim holidays.
Palestinians have said they fear that increasing visits by Jewish groups to Jerusalem's al-Aqsa mosque compound, revered by Jews as the site of Biblical temples, are eroding Muslim religious control there.
Israel has pledged to maintain Muslim prayer rights at al-Aqsa, but, citing security concerns, has frequently banned young Muslim men from entering the area, which it captured when it seized East Jerusalem and the West Bank in a 1967 war.
Earlier in the week, the White House said it was deeply concerned about the violence at the site and has called on all sides to "exercise restraint and refrain from provocative actions and rhetoric".
While violence in the occupied West Bank and East Jerusalem has not approached the levels of past Palestinian uprisings, there has been a surge of Palestinian stone-throwing.