Nassim Abou Fouda, 26, succumbed to his wounds after being shot in the head in the Israeli-occupied city, the ministry announced.
Palestinian media reported Abu Fouda was in a vehicle in central Hebron near the Ibrahimi Mosque when soldiers at a military checkpoint opened fire on him.
Over the past year, Israeli violence against Palestinians in the occupied West Bank has been getting more deadly and frequent, prompting a rise in armed Palestinian resistance.
In recent days, tensions have been at a high, after an Israeli raid on Jenin refugee camp on Thursday killed ten Palestinians. The next day, a Palestinian killed eight Israelis in a settlement in occupied East Jerusalem.
At least 35 Palestinians have been killed by Israeli troops since the beginning of January.
Last year, more Palestinians were killed by Israeli forces in the West Bank and East Jerusalem than in any single calendar year since the Second Intifada.
At least 220 people died in Israeli attacks across the occupied territories in 2022, including 48 children. Of the total death toll, 167 were from the West Bank and East Jerusalem, and 53 were from the Gaza Strip.
Meanwhile, last year Palestinians killed at least 29 Israelis, including one child, the highest death toll since 2008.