The strikes, the army said, were conducted in response to Hamas-instigated violence along the security fence at the Israeli-Gaza border, and to the cross-border arson attacks which, the IDF claimed, damages Israeli land on a daily basis.
Around 10 other passers-by were wounded, the officials said. On Friday, after an Israeli soldier was mildly wounded by a Palestinian protester who threw a hand-grenade Israel retaliated by striking "Hamas targets".
It was the largest daytime attack by Israel on the coastal enclave controlled by the Hamas Islamist group since the 2014 Israel-Gaza war, an army spokesman said.
At least one ceasefire was brokered during the fighting, reportedly by Egypt, but was quickly violated by the Palestinians.
Palestinian media said IDF planes hit targets at several sites around the Gaza strip, including a Hamas terror base. According to the IDF, the strikes also targeted Hamas naval facilities.
Still, it was unclear whether the truce would hold as warning sirens were heard in southern Israel early Sunday, indicating incoming fire, AP said.
"The protection and the defence of our people is a national duty and a strategic choice", Barhoum said.
Relatives of 15-year-old Othman Hilles mourn during his funeral in the family home in Gaza City Saturday
Three Israelis were wounded when a rocket hit a house in the city of Sderot near the Gaza Strip, authorities said.
Israel's Intelligence Minister Israel Katz said the air strikes were meant to put an end to such attacks but should not be seen as the start of a military campaign against the Palestinian territory of 2 million, devastated by seven weeks of war with Israel four years ago.
In advance of Friday's protest, the organising committee called on Palestinians to take part in the protests to express solidarity with Khan al-Ahmar, a Bedouin village in the occupied West Bank slated for total demolition by Israeli authorities.
On Friday, thousands of Palestinians gathered near the Gaza border for their near-weekly protest.
Molotov cocktails, flaming tyres and stones were also hurled in the direction of its soldiers, according to the Israeli army.
With Israel focused on rising tension along its northern border in its efforts to prevent Iran from establishing a permanent military foothold in post-civil war Syria, it has been wary of escalating hostilities in Gaza.
Gaza health officials say more than 130 Palestinians were killed and 15,000 others injured by Israeli forces during the protests.
"We are talking about the biggest offensive strikes since Protective Edge", Air Force Brigadier General Tzvika Haimovic told journalists, referring to Israel's name for its 2014 operation in the Gaza Strip.