The attack was the first by Israel in the Gaza Strip since early morning artillery fire killed 18 Palestinians, 13 of them women and children, in the northern town of Beit Hanun, drawing world-wide condemnation.
The air strike killed Ramdi Shwaber of the Mujahedeen Brigades, a group loosely affiliated with president Mahmud Abbas's Fatah faction, and Ahmad Awad of the armed wing of Hamas, the Palestinian ruling movement.
Initial reports said that one gunman, from the radical Islamic Jihad militant group, was killed in the strike.
The army confirmed the raid, saying it had targeted a car that was reportedly carrying a Hamas militant who was known for making home-made rockets that Gaza militants regularly fire into Israel.
Defence Minister Amir Peretz ordered a halt to artillery fire in the coastal strip following the deaths in Beit Hanun, but officials said a four-month offensive on Palestinian militants in Gaza would continue.
The air strike late Wednesday brought the day's toll in the Gaza Strip to 22. Earlier two Palestinians, including a Hamas gunman, were killed in the Jabaliya refugee camp.
In the occupied West Bank, a pre-dawn Israeli raid near the flash-point city of Jenin killed five Palestinians, including four militants.
The deaths bring to 5,557 the number of people killed since the start of the second Palestinian uprising in September 2000, the vast majority of them Palestinians, according to an AFP count.

Copyright AFP (Agence France-Presse), 2006