The Israeli military said the soldiers did not fire live ammunition, but used riot control weapons such as teargas and rubber-coated bullets to disperse the Palestinians who were approaching a nearby Jewish settlement.
However, sources have told Al Jazeera that Qadus was shot and killed by two live bullets to his chest.
The clashes also seriously injured another 16-year-old Palestinian boy, identified as Useid Abed an-Nasser Qadus, the cousin of the dead boy.
Medical sources said was shot in the head and was transferred to a hospital for emergency surgery.
An Israeli military spokesman insisted that both injured Palestinians were hurt by riot-control weapons rather than live fire.
The spokesman said the incident came amid "a violent and illegal riot" near Iraq Burin, during which dozens of rock-hurling Palestinians approached Bracha, a nearby settlement.
One "rock-hurler" was arrested, he added.
Clashes take place in the village on a nearly weekly basis over a water well that Palestinians claim Jewish settlers are trying to seize for their own use.
The fatality was the first during a string of clashesthat erupted this week following of Israel's consecration of an ancient synagogue in the Old City of Jerusalem and would likely increase tensions.
The death has overshadowed a visit by Ban Ki-moon,the UN secretary-general, to the Palestinian territories to reiterate the commitment of the Quartet of Middle East negotiators' to an independent Palestinian state.
The Quartet - which brings together the United Nations, the European Union, Russia and the US - had issued a statement condemning Israeli settlement building and calling for a peace deal by 2014 after a meeting in Moscow the previous day.
Following Israel's announcement of 1,600 new housing unitsfor a development in East Jerusalem last week, the Palestinian Authority pulled out of planned "proximity" talks demanding a complete halt to settlement activity.