The fire was discovered in the mosque in Jaba village at about 4:00 am (local time) yesterday. Villagers managed to put it out but there was some damage to the building, the witnesses said.
On a nearby wall, the perpetrators had sprayed the word "revenge" and other slogans in Hebrew alongside a Star of David, with witnesses saying it was believed to be the work of hardline Jewish settlers.
The village is located 10 kilometres southwest of Bethlehem, close to Gush Etzion, a cluster of Jewish settlements.
The Palestinian foreign ministry said the attack was tantamount to "an official declaration of religious war," the official WAFA news agency reported.
"This new attack is a sign of the mounting violent extremism within Israeli society," it said.
The United Nations also condemned the attack.