The resistance organisation Islamic Jihad has claimed responsibility for the attack early on Friday.
Elsewhere in the West Bank, at least three Palestinians have been wounded in clashes with Israeli occupation forces.
In a pre-dawn attack in Nablus near the site known to Jewish groups as Joseph’s Tomb, Palestinian fighters opened fire and threw an explosive device at a vehicle carrying a group of settlers, Aljazeera’s correspondent reported on Friday.
The Jewish settlers group comprised members of the Bratslav Hasidic sect, Israeli media said. They had reportedly entered the tomb along with other worshippers to pray at the site and were attacked as they left.
An earlier report said that one of the settlers had died.
Clashes later broke out between Israeli troops called into the area and local resistance fighters, the correspondent said, but there were no reports of casualties
At least two of the Jews were taken to hospital but the others were arrested for entering the Palestinian area without Israeli army authorisation, the Haaretz newspaper’s website said.
Bratslav Hasidic Jews often ignore military orders and sneak into the site of the tomb to hold prayers, it added.
West Bank settlers are among the most extreme Jews and move around heavily armed.
The tomb, an Ottoman structure dedicated to the Prophet Yusuf (the Arabic for Joseph), was reoccupied by Israeli troops after the outbreak of the Al-Aqsa Intifada in September 2000, to be followed by the rest of the West Bank.
The mosque used to attract Muslims from all over the Bilad al-Sham (the Levant) until the Israeli conquest of the West Bank in 1967 when it was taken over by Jewish settlers who later built a small synagogue there. Muslims were prevented from entering.
Following the Oslo accords, in 1993 the site was handed back to the Palestinians and Jews barred from entering for security reasons.
When the accords collapsed shortly before the Al-Aqsa Intifada started in September 2000 the site - located in the heart of the Arab city of Nablus - reverted to Israeli military rule.
Meanwhile, dozens of Israeli armoured vehicles launched a pre-dawn raid into the town of Jenin and the nearby village of Jaba, an Aljazeera reporter said.
At least three Palestinians were injured in ensuing clashes in Jaba, he added, but ambulances were prevented from reaching the village.