Mohammad Al-Bayyed, 17, from the Al-Jalazoun refugee camp, north of Ramallah, succumbed to his critical head wounds shortly after he was taken to hospital, the ministry said in a press release.
Another teen was injured in confrontations with Israeli forces following an Israeli military incursion into the Umm Safa Village, it added.
Dozens of Palestinians pelted stones at Israeli forces while trying to move into the village, which has been under continued attacks by Jewish settlers for several weeks.