According to Israel's Channel 7, around 1,500 Jewish settlers performed prayers at Joseph's Tomb under the protection of the Israeli army.
A number of Israeli troops even joined the religious rituals held on the occasion of the Jewish Hanukkah festival, the channel said.
The incursion prompted clashes between dozens of young Palestinians and the Israeli army, eyewitnesses told The Anadolu Agency.
Israeli soldiers fired teargas and rubber bullets to disperse Palestinian demonstrators who had gathered to protest the settlers' presence at the site, the witnesses said, noting that at least three Palestinians were injured during the violence.
Jews believe the site – a traditional flashpoint for violence – is the burial place of the biblical patriarch Joseph.
Muslims, however, challenge the claim, saying the tomb is the final resting place of a Muslim cleric – Sheikh Yussef Dawiqat – who died two centuries ago.