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.
Troops then "killed him in cold blood, and without him having given any resistance," she said.
"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.
One man attacked a soldier, who in response shot him in a lower limb. The wounded man was taken to hospital, she 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.
The army said petrol bombs were also thrown, and soldiers responded with rubber bullets.
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.
An army spokeswoman said he had been involved in a shooting attacks against the army, and was being held in custody by the Palestinian Authority, but constantly violating the terms of his custody.
Abu Riyala, in his mid-20s, was shot while attempting to escape his arrest, she said.
- 'Damaging climate' -
Israeli authorities say the arrest raids are necessary to detain suspects and that troops can face dangerous rioting during the operations.
Palestinians, however, condemn the raids in the occupied territories, and the Hamas and Islamic Jihad militant groups hinted at revenge after Thursday's death.
"We hold the Zionist occupation's forces totally responsible for the killing of the martyr Falah Abu Maria in cold blood," they said in a joint statement.
"The two movements stress our people's right to self-defence and to a response to the crimes of the occupation, by all possible and available means.
The shootings came after weeks of violence in the Palestinian territories, and amid regular Israeli arrest operations.
The deaths "aim to undermine stability and to create a climate of tension in the region," official Palestinian news agency Wafa quoted president Mahmud Abbas's spokesman as saying.
"Stop creating this damaging climate immediately," he added, referring to Israel.
Last month, soldiers shot dead a Palestinian who opened fire at troops at a checkpoint in the Jordan Valley during the Muslim fasting month of Ramadan.
Also in June, a Palestinian stabbed an Israeli policeman in Israeli-annexed east Jerusalem's Old City, before being shot and wounded.
Last week, Israel arrested five Palestinians suspected of involvement in the murder of an Israeli who was shot in his car in the occupied West Bank.
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