The main target on Monday appeared to be Mahmud Abu Khalifa, a leader of the al-Aqsa Martyrs' Brigades, a group linked to Yasir Arafat's Fatah movement.
He was killed along with Amjad Husni and Yamin Abu al-Hasan who were also members of the same resistance group.
"I heard a large explosion and saw the car totally burned. People in the area pulled out three bodies from the car," said witness Hasan Jara.
Palestinians said Abu Khalifa was the deputy to Zakaria Zubaidi, local commander of the al-Aqsa group.
Zubaidi immediately vowed to carry out revenge attacks for the killing of the three men. "This attack will not pass in silence and our response will be in Tel Aviv in the next 24 hours," he told reporters.
"Three Palestinian passer-by children were wounded during the Israeli helicopter strike", said Al Jazeera's correspondent in Jenin.
"The car and the bodies were completely burnt so it was very difficult to get the bodies out of the car. The disfigured bodies were transported to the city's hospital."
The Israeli military refused to comment.
Abu Khalifa and Husni had escaped an Israeli air strike in the
northern West Bank town on 30 August.
It was the first Israeli air attack on Palestinian fighters since combat aircraft killed 16 members of the resistance movement Hamas while they were undergoing military training on a football pitch in the eastern Gaza Strip.
"This attack will not pass in silence and our response will be in Tel Aviv in the next 24 hours"
During four years of the Palestinian Intifada, Israel has killed dozens of Palestinian resistance fighters in air strikes. Scores of bystanders have also been killed and wounded.
Israel defends the practice as self-defence, saying it is preventing Palestinian attacks. Palestinians and human rights groups denounce it as summary execution.