Obeid al-Ghirbali and Muhammad Harara were named as those killed, medical spokesman Adham Abu Salmiyeh said.
Both men were members of the Al-Quds Brigade, the armed wing of Islamic Jihad. Their bodies were taken to Dar al-Shifa hospital.
Israel’s army said in a statement that it had “thwarted two terrorist squads from firing rockets at Israel from the northern and the central Gaza Strip.”
Earlier, an Israeli strike targeting a car in western Gaza killed the head of the Popular Resistance Committees and a former prisoner released by Israel four years ago, medical officials said.
Israel accused PRC secretary-general Zuhair Qaisi, one of the men killed, of helping to plan attacks along its border with Egypt that killed seven Israelis last year.
The PRC has denied involvement in that cross-border attack.
The Israeli military said militants fired eight rockets in all on Friday.
The national resistance brigades, the DFLP’s armed wing, the Al-Aqsa brigades, and the armed wing of the PRC, the An-Nasser Salah Ad-Din brigades, have all claimed responsibility for rocket fire.
Presidential spokesman Nabil Abu Rudeineh condemned the earlier Israeli airstrike, saying it will lead to an escalating cycle of violence in the region.
Hamas’ foreign ministry called on the international community to intervene to stop Israeli aggression against the Palestinian people, a statement said.
The An-Nasser Salah Ad-Din Brigades, the PRC’s armed wing, had promised a “seismic response” to the earlier assassination.