At least two Palestinians threw a Molotov cocktail at a military jeep on patrol close to Halhul north of the West Bank city of Hebron, a military spokeswoman said.
Responding to an "immediate threat", the soldiers fired on them, killing one. The other was arrested, she said.
The Palestinian health ministry confirmed the death, identifying him as 17-year-old Haitham al-Bau.
His death brings to 165 the number of Palestinians killed by Israeli forces in four months of violence. More than half of them were alleged assailants, while others were killed during protests.
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Elsewhere today clashes erupted during a new "day of rage".
Near Ramallah in the West Bank, clashes broke out as around 100 youths threw stones at Israeli soldiers who responded with live fire after using tear gas and rubber bullets, an AFP journalist said.
Clashes were also taking place along the border between the Gaza Strip and Israel, AFP journalists said.
Protests are common on Fridays in the West Bank, which Israel has occupied since 1967.