Aljazeera, quoting Palestinian medical sources, said the fighters, who belonged to Islamic Jihad's al-Quds Brigades, were killed inside a car late on Friday in northern Gaza.
Islamic Jihad identified the dead men as Emad Yassin and Habib Ashour.
An Israeli army spokeswoman said the air strike targeted "a car between Gaza City and the Deir al-Balah camp carrying an Islamic Jihad cell responsible for the firing of rockets into Israel". The army says 120 rockets have been fired in southern Israel in the past week.
Israel's Army Radio said Yassin was one of Islamic Jihad's top operatives in the Gaza Strip and was responsible for many of the rocket attacks against Israel in recent days.
Earlier in the day, Palestinian fighters had fired five homemade rockets into Israel but the army reported that no injuries were caused by the attacks.
Earlier, Hamas fighters distanced themselves from a ceasefire offer that the Palestinian government led by the Islamic resistance movement made to Israel, while other armed groups also rejected the proposal.
The offer, which was conditional on Israel stopping raids and air strikes in Gaza and the West Bank, failed due to differences between factions in Hamas. The group's armed wing scrapped a 16-month truce with Israel a week ago and soon after launched a barrage of makeshift rockets from the Gaza Strip.
But a government spokesman made a new ceasefire offer on Thursday.
"We are not interested in making any offers or proposals," said Sami Abu Zuhri, official spokesman for the Hamas movement.
"When the occupation stops its killings and crimes against our people then the factions may look into the issue in accordance with the interests of our people."