It was the second killing in 24 hours of a Palestinian during an arrest operation, and came amid weeks of low-level violence.
Falah Abu Maria, 50, was shot in the chest at his home in Beit Omar village near the southern city of Hebron, neighbours said.
He had run to the upstairs balcony to call for an ambulance after his son Mohammed was wounded while being arrested by the army, wife Fayqa told AFP.
"We didn't do anything to them. He went out onto the balcony calling for an ambulance, and they opened fire on him... And killed him," she said.
The hospital said 24-year-old Mohammed was being treated for a gunshot wound to the pelvis.
The Israeli army said troops faced attacks with bricks and stones during the operation to arrest Mohammed, who was wanted on suspicion of unspecified security offences.
"Forces were attacked by a violent mob" as they tried to detain him, an army spokeswoman said.
She could not confirm his identity but acknowledged the wanted suspect was not taken into custody.
"As the forces left the scene, they were attacked once again by a violent mob who hurled rocks and bricks at them," she said. "The forces responded with fire towards the main instigator."
A soldier was "slightly injured" by a stone, she said.
Falah Abu Maria was buried in his village, where stone-throwing youths clashed with the army afterwards.
One Palestinian fired a rifle at the forces, an AFP correspondent said.
There were no reports of casualties.
The incident was similar to one on Wednesday near the northern West Bank city of Jenin, where troops shot dead Mohammed Alawneh, 22, in clashes that followed raids and searches at several houses in the village of Birqin.
Alawneh was shot in the chest and died shortly after arriving at hospital in Jenin, according to a Palestinian medic.
Also Thursday, Israeli forces raided a residential building in the northern West Bank city of Nablus, where according to Palestinian witnesses they shot and then arrested Mustafa Abu Riyala, sparking clashes.
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