Explosives destroyed the apartment of Omar Jaradat in Silat al-Harithiya village, near the flashpoint town of Jenin in the northern occupied West Bank, according to a statement by the Israeli army.
It said Palestinians clashed with Israeli forces, throwing stones and firebombs, which soldiers responded to with semi-automatic fire.
Two Palestinians were wounded, according to an AFP photographer at the scene.
The clashes add to tensions in Israel and the West Bank as a large-scale manhunt continued for a pair of Palestinians suspected of killing three Israelis in an axe attack Thursday night near Tel Aviv.
Over the past month police and Palestinians have also clashed at the Al-Aqsa mosque compound in Jerusalem’s Israeli-annexed Old City.
Explosives punched a hole in the pink exterior wall of Jaradat’s apartment and blew out interior walls, leaving the floors strewn with grey rubble.
Israel accused Jaradat and two of his family members of killing religious student Yehuda Dimentman, 25, on December 16, 2021. Gunmen sprayed a car with bullets as it drove out of the wildcat settlement outpost of Homesh. Two others were wounded in the attack.
Security forces have previously demolished three other homes of Jaradat family members in Silat al-Harithiya.
Those operations in February and March also led to clashes, in which the army shot dead a Palestinian teenager.
Israel regularly destroys the homes of individuals it blames for attacks on Israelis.
The practice has been condemned by critics as a form of collective punishment. Israel insists it deters attacks.
Around 475,000 Jewish settlers live in the West Bank in communities widely regarded as illegal under international law, alongside around 2.9 million Palestinians,
A string of anti-Israeli attacks since March 22 have killed 18 people, including an Arab-Israeli police officer and two Ukrainians.
Two of the deadly attacks were carried out in the Tel Aviv area by Palestinians.
A total of 27 Palestinians and three Israeli Arabs have died during the same period, among them perpetrators of attacks and those killed by Israeli security forces in West Bank operations.