After the strikes balls of flame shot into the air, leaving dark smoke drifting over the territory.
Hamas spokesman Hazem Qassem said the air raids, in the southeast of Gaza City, "are an extension of the aggression against Palestinian territory in Jerusalem and the occupied West Bank," after the killing of three Palestinians on Friday.
Twelve Palestinians were also wounded in that same incident during an Israeli army raid in Jenin, a stronghold of armed Palestinian factions in the West Bank.
The men were killed when Israeli forces opened fire on their vehicle, the Palestinian news agency Wafa said.
Israel's army said soldiers had come under fire during an operation to search for weapons.
One of the dead was a Hamas commander, the group said, vowing that the killings "will not go unpunished".
Qassem made no mention of whether Saturday's air strikes caused any casualties.
Israel's army said hours earlier that air raid sirens sounded in the southern Israeli city of Ashkelon and in areas near the blockaded Gaza Strip.
In April, Israeli warplanes also hit Gaza after Palestinian armed groups fired rockets from the territory.
That exchange came after nearly a month of deadly violence focused on Israeli-annexed east Jerusalem's flashpoint Al-Aqsa mosque compound, the third holiest site in Islam.
The impoverished Hamas-controlled Gaza coastal enclave of 2.3 million people has been under an Israeli blockade since 2007.
Last year, Israel and Hamas fought an 11-day war triggered in part by unrest over the Al-Aqsa mosque compound, the most holy site for Jews, who call it the Temple Mount.
Israel occupied the West Bank and east Jerusalem in the 1967 Six-Day War. It later annexed east Jerusalem in a move never recognised by most of the international community.