"Rocks were hurled at the soldiers, wounding one of them lightly," a spokeswoman told AFP, adding that the soldiers first fired warning shots "and then (fired) toward the suspect resulting in his death."
The incident occurred in the Beit Ummar area near the city of Hebron.
The Palestinian health ministry named the dead stronethrower as Khaled Bahar, 15.
Violence since October 2015 has killed 235 Palestinians, 36 Israelis, two Americans, one Jordanian, an Eritrean and a Sudanese national, according to an AFP count.
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Others were shot dead during protests or clashes, while some were killed in Israeli air strikes on the Gaza Strip.
Israeli police today defended officers who shot dead a 19-year-old Palestinian accused of trying to stab them, after video emerged appearing to show them fire at her as she lay on the ground.
Police said an inquiry had been opened into the yesterday shooting, as is usually done with fatal incidents.
"The video shows a partial picture of the event," police spokeswoman Luba Samri said in a statement.
"From the recording of the event it is possible to see that immediately after the danger was neutralised and had passed, the officers stopped firing, closed the area and proceeded to do the follow-ups on the incident."
The Palestinian foreign ministry harshly criticised yesterday's shooting, saying in a statement that "the recording shows the soldiers continued to shoot her despite her falling to the ground and not representing any threat to them."
The incidents came as Jews celebrated the week-long holiday of Sukkot, the third of three successive Jewish holidays that have led to tensions with the Palestinians in the past.
The sensitive compound is holy to both Muslims and Jews, who refer to it as the Temple Mount.
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