Scuffles broke out between Israeli troops and Palestinians in the West Bank, as Muslims tried reach a holy shrine on the first Friday of Ramadan.
Israel has constructed a massive barrier around east Jerusalem
Hundreds waited at checkpoints north and south of Jerusalem after Israel imposed tighter security than usual.
Only men aged over 45 were allowed to enter Jerusalem for prayers at the al-Aqsa mosque in the Old City.
Israel said curbs on movement were essential for security but Palestinians denounced it as collective punishment.
This year the first Friday of Ramadan coincides with the Jewish New Year holiday.
Both are times when Israel customarily increases its security clampdown in the occupied territories, fearing militant attacks.
Palestinians have long complained it is a violation of their freedom of worship.
Palestinians needed to obtain special permits to enter the al-Aqsa mosque, which is the third holiest shrine in Islam as well as being revered by Jews as the Temple Mount. Only women over 35 were allowed in.
Between Bethlehem and Jerusalem, hundreds of Palestinians pushed up against a police cordon, at one point pushing through it.
Israel has constructed a massive barrier around Jerusalem and controls Palestinian access from the Israeli-occupied West Bank and some parts of occupied East Jerusalem through a number of checkpoints.
The Jewish state claims the whole of Jerusalem as its capital but the Palestinians want the eastern side - occupied by Israel in 1967 - as the capital of their future state.