Authorities also said 66 people had been arrested in Jerusalem over the past week, including some detained in connection with the unrest at Al-Aqsa which saw Israeli police clash with rioters.
Yom Kippur begins tomorrow night and lasts until Wednesday evening, with thousands of Jews expected to visit the Western Wall below the Al-Aqsa compound in Jerusalem's Old City.
The Muslim Eid al-Adha holiday begins on Wednesday evening and continues until Sunday.
The Al-Aqsa compound will be open to visits as usual on Wednesday, but only Muslims will be allowed access during the four-day Eid holiday, police said.
Israeli authorities said they would decide tomorrow whether to impose age restrictions on Muslims entering the compound. They have previously prevented younger people from entering to reduce the risk of violence when tensions have run high.
Last week's clashes occurred as Jews celebrated their New Year, or Rosh Hashanah.
Police said they raided the Al-Aqsa compound to stop youths who had barricaded themselves inside the mosque from disrupting visits by Jews and tourists.
There were also clashes in the alleyways of the Old City outside the compound. Friday saw further unrest in the occupied West Bank and sporadically in Jerusalem.
Al-Aqsa, the third holiest site in Islam, is also venerated by Jews as the Temple Mount and is considered the most sacred in Judaism.
Muslims have been alarmed by an increase in visits by Jews to the site and fear rules governing the compound will be changed. Jews are allowed to visit but not to pray to avoid provoking tensions.