The air strikes on Tuesday were the latest incident in more than a year of surging violence that has seen repeated Israeli military raids and escalating settler violence in the occupied West Bank, amid a spate of Palestinian street attacks targeting Israelis.
Israel's military said it targeted three senior commanders of Islamic Jihad, the second-most powerful armed group in the blockaded coastal enclave, which is controlled by the Islamist militant group, Hamas.
"Any terrorist who harms Israeli citizens will be made to regret it," said Defence Minister Yoav Gallant.
Israel's military, working with the Shin Bet intelligence service, targeted the leadership of the Islamic Jihad in Gaza in a "precise" operation, he added.
A Gaza health official said at least 12 people had been killed and 20 more wounded in air strikes that hit residential areas.
Islamic Jihad's armed wing confirmed the three deaths, adding: "We will not abandon our positions and the resistance will continue, God willing."
The group identified the commanders killed as Jihad Ghannam, Khalil Al-Bahtini and Tareq Izzeldeen.
Powerful explosions rocked the area for hours as witnesses reported Israeli jets hitting Islamic Jihad shelters in residential areas and sites across the Gaza strip, including training camps and border posts.
"The bombardment will be met by bombardment and the attack will be met by an attack," said Tareq Selmi, a spokesman of Islamic Jihad.Â
"This crime will not pass unpunished."
Videos showed billowing smoke and flames that lit up the night sky as trucks of firefighters sped to a building that had been hit, while a medic reassured a young girl who appeared confused.
"Your family is all safe, don't worry," he said.
During the bombardment, Palestinians took to social media to mourn a well-known dentist who was killed at home with his wife in Tuesday's air strikes, describing him as a loyal friend and humble man.
Last week, the death of a Palestinian hunger striker in Israeli custody triggered several hours of cross-border fighting between Israel and armed groups in Gaza, in which one Palestinian man was killed.
More than 100 Palestinians and at least 19 Israelis and foreigners have been killed in the strife since January.
COGAT, a unit of the Israeli defence ministry that coordinates civilian affairs with the Palestinians, said its two Gaza crossings were closed to people and goods until further notice.
In anticipation of rocket fire in response to the killings, Israel's military urged citizens living in towns within 40 kilometres of Gaza to stay near bomb shelters.
