The strike was carried out on a Hamas post in Nusseirat in the central Gaza Strip amid violence that erupted following US President Donald Trump's controversial recognition of Jerusalem as Israel's capital.
A fresh Israeli air strike in the Gaza Strip killed two people on Saturday, the Palestinian Health Ministry said.
The strike on a Hamas post in Nusseirat in the central Gaza Strip, one of several in the early hours, came amid protests across the Palestinian territories against US President Donald Trump's deeply controversial recognition of Jerusalem as Israel's capital.
In a statement, ministry spokesman Ashraf al Qudra said two Palestinians were recovered from under the rubble of the post hit by Israeli warplanes.
The two men named as Abdullah al Atal, 28 and Mohammed al Safdi, 30, according to the statement.
The officials did not say if the dead men were Hamas members.
TRT World spoke to journalist Mohammad Mansour from Gaza for the latest.
"Children and women injured"
Israeli officials said that the strike followed three rocket attacks Friday night from Gaza into southern Israel.
"Today, in response to the rockets fired at southern Israeli communities throughout yesterday, Israel air force aircraft targeted four facilities belonging to the Hamas in the Gaza Strip," an English-language army statement said on Saturday.
It alleged the targets were "two weapons manufacturing sites, a weapons warehouse and a military compound."
"In each target, several components were hit," it added.
Israeli strikes on Hamas facilities on Friday night wounded 14 people, among them women and children, the Hamas medical services said.
Israeli officials said they followed three rocket attacks during Friday's Palestinian "day of rage" over Trump's decision.
In one of them, a rocket hit the southern Israeli city of Sderot although Israeli public radio said it did not explode and did not cause any casualties.
The Israeli military said that its Iron Dome air defence system intercepted an earlier rocket fired from the Palestinian enclave.
It said it later detected a second missile launch, but had not found evidence that it had reached Israeli territory.
The military retaliated Friday with air strikes on what it said were two targets.
"In response to the projectiles fired at Israel from the Gaza Strip earlier today, Israel air force aircraft targeted a Hamas training compound and an ammunition warehouse in the Gaza Strip," an English-language statement said.
Gaza security officials said that both targets were in the vicinity of Beit Lahiya, in the northern part of the strip, close to the border with Israel.
A group calling itself the Salahedin Brigades claimed responsibility for one of the attacks.
But the Israeli army said it held Hamas responsible for all "hostile activity" originating from the territory under its control.
Tension has risen across the West Bank and Gaza following Trump’s decision on Wednesday to recognise Jerusalem as Israel’s capital.
Thousands of Palestinians staged rallies across the West Bank amid clashes with Israeli forces, which killed at least two protesters and wounded hundreds.
Jerusalem remains at the heart of the Israel-Palestine conflict, with Palestinians hoping that East Jerusalem - occupied by Israel in 1967 - might eventually serve as the capital of a future Palestinian state.