The Islamic Jihad's top bomb-maker was among the two killed on Sunday night in the Zeitun neighbourhood of Gaza City, the sources and medics at the scene said.
Sources in Islamic Jihad confirmed that Adnan Bustan, 28, who headed the armed group's "engineering and manufacturing unit" that produces rockets and explosives, had been killed in the Israeli raid.
The other killed was named as Jihad al-Sawafiri, 31.
Their deaths brought to 4944 the overall toll since the September 2000 launch of the intifada, the majority of them Palestinian, according to an AFP tally.
The raid followed the killing of three Palestinian fighters overnight in Israel's first air strike on the Gaza Strip since Islamist group Hamas' sweeping victory in parliamentary elections last month.
Hundreds of armed men among the mourners for the three men at a funeral on Sunday threatened to carry out revenge attacks.
Israel claimed the strike was meant to deter rocket attacks on Israel from the Gaza Strip, such as one that wounded three settlers in southern Israel on Friday.
And only hours before this, Israeli military had fired dozens of artillery rounds at northern Gaza and eastern Gaza City.