The Iran-backed Palestinian Islamic Jihad group confirmed the death of Bahaa Abu al-Ata, 42, and his wife Asma Mohammed, 39 in an Israeli hit on their home at dawn.
In retaliation, fighters fired nearly 200 rockets at Israel, with sirens blaring as far north as the country’s commercial capital Tel Aviv. Israel responded with strikes across the strip, which killed five people in total, including Abu al-Ata.
Islamic Jihad said Abu the commander was undergoing “a heroic act” when he was assassinated but did not elaborate. Its senior leader Ziad al-Nakhala added that the killing “crossed all red lines”, announcing that the fighters “are going to war”.
The group also claimed Israel targeted the house of Islamic Jihad political leader Akram Al-Ajouri in Damascus, Syria, killing one of his sons overnight.
Syrian state media earlier reported that at least two people were killed and six wounded in an attack in the early hours that targeted a building in the capital.
In Israel, Prime Minister Benjamin Netanyahu called Abu al-Ata, an “arch-terrorist ... the main generator of terrorism from the Gaza Strip.”
“He was in the midst of plotting additional attacks these very days. He was a ticking bomb,” Mr Netanyahu said, adding that the decision to target the leader was taken 10 days prior to the strike.
Military spokesman Lt Col Jonathan Conricus said fighter jets conducted a dawn “surgical strike” on a building in Shajaiya, northern Gaza, against the leader who they believed was planning an imminent attack on Israel.
It marked Israel’s first targeted killing in the Strip since May, when they took out Hamid Abdul Khudri, an alleged financier for Gaza’s militant group Hamas, in a missile attack on his car.
“At approximately 4am, we conducted a surgical strike and ... [were] able to take care of an immediate threat, a ticking bomb, conducting a pre-emptive strike aimed to kill a senior military commander,” he told reporters.
“We have intelligence he was trying to conduct an attack in the coming days. A combination of sniper, IEDs and rocket fire aimed at Israeli troops possibly Israeli civilians,” he added.
Lt Col Conricus confirmed that the military had deployed additional tactical forces to bolster their defences against a possible ground attack and called up a few hundred reservists, from the Iron Dome missile defense units and Military Intelligence.
He said that while Israel had no plans to resume a programme of targeted killings, the flare-up had “the hallmarks of an extended event.”
In line with Israeli military policy, he would not comment on the Damascus airstrikes.
Egyptian officials in Cairo said they were working on deescalating tensions, and had opened up channels with the US as well as the European Union.
The sudden flare up comes at a tense time politically for Israel, as Mr Netanyahu leads a caretaker government after two inconclusive elections.
While many in Israel welcomed the action, some political opponents accused the leader of using the Gaza strike to win support and “save his own skin” after he failed to form a broad coalition government.
His main rival, former army chief, Benny Gantz – who supports the Gaza strikes – currently has the mandate to build a ruling coalition and has been negotiating with party allies for several weeks.
A successful military operation could not only bolster Mr Netanyahu, as he struggles to cling on to power, but might help him stay in office; if Israel's attorney general decides to go ahead with indicting him in several corruption cases in the coming weeks.
“To save his own skin, Netanyahu turns to the only thing he can do: killing, destruction and warmongering,” Ofer Cassif, a parliamentarian with the mostly-Arab Joint List, tweeted.
“The bloodshed is on his head,” he added.
The Israeli army denied the timing was political. The killing of the senior Islamic Jihad commander also poses a challenge for Hamas, the militant group that runs Gaza and has tried to maintain a fragile truce with Israel over the last few years. After the attack Hamas released a statement saying Israel “bears full responsibility for all consequences of this escalation” – pledging that Abu al-Ata’s death “will not go unpunished”.
Islamic Jihad shares Hamas’s ideological commitment to destroy Israel. But unlike Hamas, it has often fought against Egyptian-led efforts to forge ceasefires with the Israelis.
Many of Gaza’s nearly 2 million-strong population are braced for further Israeli airstrikes, with some civilians telling The Independent they were out buying supplies in preparation for an extended campaign.
Meanwhile, major border-entry points into Gaza from Israel, including Erez passenger terminal and Kerem Shalom goods crossing, have all been closed, further piling pressure on the population.
Israel confirmed it limited Gaza’s fishing zone to six nautical miles. Hundreds attended Abu al-Ata’s funeral on Tuesday afternoon, with many chanting against Israel.
Speaking from the funeral, Abu al-Ata’s father Salim said his son had disappeared for a week after his name was circulating in Israeli media – blaming him for a barrage of rockets fired into Israel on 2 November. He added: “It’s a crime to bomb him when he is asleep at his home.”
— כאן חדשות (@kann_news)November 12, 2019
In Israel, at least one home has taken a direct hit from rocket fire, schools in the southern and central districts were closed for the first time since the war with Gaza in 2014.
Non-essential work near Gaza has also been cancelled and bomb shelters opened. Videos were shared showing a rocket hitting a road in southern Israel, narrowly missing traffic.
The EU condemned the barrage of rocket fire and called for “rapid and complete de-escalation”. Jordan meanwhile blamed Israel for the sudden outbreak of violence, saying fighting will only “deepen” despair in Gaza and “promote extremist agendas in the region.”
Over the last year, militants in Gaza and Israel’s military have teetered on the cusp of war with multiple serious cross border flare-ups, triggered in part by the start of Great March of Return protests in the 25-mile-long enclave.
Since the Gaza rallies began in March last year, much of them triggered by a 12-year-long Israeli- and Egyptian-siege on the Strip, nearly 270 Palestinians have been killed and thousands more wounded by Israeli troops.
Israel said Palestinians have repeatedly attacked the border zone and threatened citizens in southern Israel, by launching firebombs and kites tied with explosive devices.