The man died during clashes south of Bethlehem in the southern West Bank, the ministry said in a statement, without giving his name or age.
Sources from the village of Tuqu where the incident took place named the victim as Qusai al-Amour, 17, saying he had been shot in the chest.
The Israeli army said the shooting occurred during a "violent riot" in which "rioters hurled rocks" at security forces.
"Due to the extent of violence, border police fired 0.22-calibre rounds towards the main violence instigator, resulting in his death," an army spokeswoman said.
Most of the Palestinians killed were carrying out knife, gun or car-ramming attacks, according to Israeli authorities, with others killed during protests, in clashes or air raids on Gaza.
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