The students were reportedly were on their way to the Tomb of the Patriarchs when they accidentally drove into the Palestinian part of divided city, Hebron.
During the hostilities, the men were able to escape their car, which was pelted with stones and set alight, before a Palestinian man came to their aid.
Fayez Abu Hamdiyeh told Ma'an that he saw the five men running away from a group of Palestinians when he let them into his home.
He then contacted the Israeli authorities to get them out of the area.
Abu Hamdiyeh told Ynet News: "As soon as we saw that a riot was starting outside, my family and I managed to bring them inside and we quickly closed the doors."
"We gave them water to drink and tried to tell them that they were safe, but they didn't speak Arabic."
He said that he was "not a hero", adding: "I did what needed to be done."
Israeli forces later arrived to escort the Jewish students away, using tear gas, rubber bullets and stun grenades against the Palestinians.
Israeli rights group B'Tselem filmed the students being led away by armed guards.
Hebron is the largest city in the West Bank and sees frequent clashes between Palestinians and Israelis.