The air assault followed the death of a woman who was shot by a sniper in the south of Gaza.
Palestinians said an Israeli missile struck the car in northern Gaza, killing three activists of the Izz al-Din al-Qassam Brigades, the armed wing of the Hamas movement.
Imad al-Maqusi, the leader of the brigades in in Bait Lahia, was killed in the strike, Palestinian medical sources said.
The Israeli military said the vehicle was transporting weapons.
"The Israeli army carried out an aerial attack against a vehicle in the northern Gaza Strip, laden with Qassam rockets and carrying Hamas terrorists on their way to launch the rockets at Israel," an army statement said.
Israel's four-month offensive in Gaza started after a soldier was captured by Palestinian fighters.
A spokesman for the armed wing of Hamas responded to the attacks saying: "These attempts will fail [to free the missing soldiers] because we do not fear assassinations and these killings will not put pressure on us.
Israeli troops have clashed with hundreds of Palestinian worshippers at two checkpoints in the West Bank after they were stopped from entering east Jerusalem to pray.
Violence broke out at an army checkpoint of Qalandiya, between Jerusalem and Ram Allah, and at another controlling access from Bethlehem in the south.
Israeli soldiers used stun grenades and rubber bullets to disperse the crowd after stones were thrown, witnesses said. There were no reports of any injuries.
Palestinians trying to enter
Jerusalem clashed with troops
The Israeli army often relaxes restrictions on access to east Jerusalem during the holy month of Ramadan, allowing women and older men to take part in Friday prayers at the third holiest site in the Islamic world.
In a separate incident, the Foreign Press Association on Thursday accused the Israeli army of "unprovoked violence against journalists" after two Palestinian journalists were beaten up and one of them detained in the West Bank.
"In both cases there is no evidence that either colleague was doing anything other than pursuing their journalistic duties," the FPA said in a statement.
Emad Borat, a freelance cameraman for Reuters news agency, has been in custody since he was detained while filming soldiers entering the Palestinian village of Bilin on October 6, said Shai Carmeli-Pollak, a filmmaker.
Bilin, near the boundary with Israel, is the scene of weekly protests against Israel's West Bank separation barrier. Pollak said Borat was beaten up inside a military Jeep after his detention and needed six stitches for a gash on his face.
A military judge has ordered Borat to be released, but he remains in custody while prosecutors appeal against the order. The army has accused Borat of throwing stones at Israeli border police while filming, Pollak said.
Borat was the main photographer for Pollak's documentary, Bilin My Love, which won best documentary at the recent Jerusalem Film Festival.
The FPA complaint also cited the case of Jaafar Ashtiyeh, a photographer for Agence France Presse.
"In both cases there is no evidence that either colleague was doing anything other than pursuing their journalistic duties"
The Foreign Press Association statement
Ashtiyeh said an Israeli soldier chased and kicked him after he tried to take photographs of an Israeli checkpoint next to the West Bank city of Nablus.
The FPA, which represents foreign journalists in Israel, the West Bank and Gaza Strip, said both cases raised "serious concerns about the treatment of journalists by members of the Israeli armed services".
The Israeli army has not commented on the accusations.