Authorities also said 66 people had been arrested in Jerusalem during the past week, including some detained in connection with the unrest at Al-Aqsa which saw Israeli police clash with rioters.
Yom Kippur begins on Tuesday 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.
From Monday night, traffic will be restricted around the Old City and checkpoints will be set up.
The Al-Aqsa compound will be open to visits as usual on Wednesday, but Muslim men under the age of 40 will be denied access during the four-day Eid holiday, police said.
Israeli authorities re-imposed age restrictions on Muslims entering the compound to reduce the risk of violence when tensions 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.
Clashes broke out during the raids, with protesters throwing fireworks, stones and other objects at police, who fired stun grenades.
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.
Israeli Prime Minister Benjamin Netanyahu has said repeatedly he is committed to the status quo at the site.
Israel seized east Jerusalem, where Al-Aqsa is located, in the 1967 Six-Day War and later annexed it in a move never recognised by the international community.
In a further sign of tight security, Israel has also deployed two anti-missile batteries around the cities of Sderot and Netivot near the Gaza Strip, army radio reported.
Three rockets were fired into southern Israel at the weekend from the Palestinian enclave controlled by the Islamist Hamas group, without causing casualties.