Palestinian medics said the toll from the operation rose to seven overnight when a fighter from Hamas's armed wing died of his wounds.
Palestinian officials said Israeli ground forces killed four civilians.
A helicopter missile strike killed a Hamas fighter and another fighter from the Army of the Nation, an al-Qaeda-inspired Gazan faction, the officials said.
Twenty-seven people were injured in the raid.
Friday's incursion came after two Hamas fighters were killed in an overnight Israeli air raid in southern Gaza, and two days after Palestinian fighters carried out a cross-border raid in which two Israelis were killed.
Three smaller armed groups claimed responsibility for the attack, but Israel blames Hamas, which seized control of Gaza in June.
Power cut fears
Saturday marked Gaza's fourth day without fuel supplies, prompting the head of Gaza's main electricity company to warn of possible power cuts.
Israel halted fuel supplies to Gaza on Thursday, a day after the attack by Palestinian fighters on a border crossing used to pump fuel to Gaza's main power plant.
"In a few days, if the fuel supplies ... are not resumed we will be forced to shut down the entire power plant," Rafiq Maliha, the plant's director, said.
"This means we will stop feeding electricity to over half a million people living in Gaza."
A spokesman for Israel's Co-ordination and Liaison Administration in Gaza said no fuel was pumped from the terminal on Thursday or Friday.
He had no information about when shipments would be resumed.
Carter meeting
Hamas hopes to use an upcoming meeting with Jimmy Carter, the former US president, to highlight the plight of people in Gaza.
Khaled Meshaal, the exiled Hamas leader, is likely to meet Carter in the coming weeks, a Hamas official told Al Jazeera.
Sami Abu Zuhri, a Hamas spokesman, said the meeting would be an opportunity for Hamas to clarify to the West its political position.
"This step reflects the increasing western recognition of the importance of dialogue and contacts with Hamas movement," he said.
"In return, we, the Hamas movement, of course aim at clarifying our stances, protecting the rights of the Palestinian people and explaining their suffering."