Underscoring the frailty of the truce, a volley of rockets was fired from the coastal strip into the Jewish state after the deal officially took effect on Thursday morning.
Israel hit back with strikes early Friday against Islamic Jihad, the second most powerful Palestinian militant group in Gaza after Islamist movement Hamas which runs the enclave.
Hours before the ceasefire was due to begin on Thursday, Israel hit the family home of Rasmi Abu Malhous, who it described as an Islamic Jihad commander.
The strike -- in Deir al-Balah, in Gaza -- killed Abu Malhous, his two wives and five children, according to the Palestinian health ministry in the strip.
Islamic Jihad said Malhous was "known as a person affiliated with Islamic Jihad but he was not a commander".
Israeli military spokesman Jonathan Conricus said that the target, "like many others, had the tactic of hiding ammunition and military infrastructure in their own residence".
The army acknowledged civilian casualties but said they were unanticipated.
"According to the information available to the IDF (Israel Defence Forces) at the time of the strike, no civilians were expected to be harmed," it said Friday.
"The IDF is investigating the harm caused to civilians by the strike," it said in a statement to AFP.
Earlier in the week the army accused Islamic Jihad fighters of using "human shields" in an attempt to discourage Israel attacking.
Survivors of the strike targeting Abu Malhous, including more of his children, were taken to a local hospital.
"They are innocents and they will have only painful memories. It will take time for them to recover," Eid Abu Malhous, a relative who tried to comfort survivors, told AFP.
The latest round of fighting began on Tuesday when an Israeli strike killed a top Islamic Jihad commander, Baha Abu al-Ata, and his wife and brought a wave of rocket fire into Israel in response.
Israel said that he had been the brains behind many operations against the Jewish state. Although smaller than Hamas, Islamic Jihad is considered more radical.
Following his death Islamic Jihad launched more than 450 rockets into Israel, causing injuries and property damage but no casualties.
The barrage set air raid sirens wailing and sent Israelis rushing to bomb shelters in the country's south and central regions, including the economic capital, Tel Aviv.
One rocket narrowly missed speeding cars on a busy highway.
Israeli air defences intercepted dozens of rockets, exploding in fireballs high in the sky.
Israel responded with a series of strikes on Gaza that killed a total of 34 Palestinians and wounded more than a hundred.
It was the deadliest surge in violence in Gaza since May 2018 when border clashes sparked by the opening of the US embassy in Jerusalem left about 60 Palestinians dead from Israeli army fire.
Friday's Israeli strikes, against what was described as a "rocket production site", left at least two wounded on the Palestinian side, the Gaza health ministry said.
It came after at least seven rockets were fired at Israel from Gaza Thursday, which Israel said it viewed "with great severity".
Israel said it was prepared to "continue operating as necessary against all attempts to harm Israel civilians".
The ceasefire brokered by Egyptian and UN officials, the usual mediators between Gaza and Israel, was agreed as the flare-up raised fears of a new all-out conflict.
To keep a lid on tensions, Palestinians cancelled weekly protests along the Gaza-Israeli border that have often led to violence since March 2018.
The violence came at a politically sensitive time for Israel, with no new government in place since a September election ended in deadlock.
Unusually, Israel has singled out Islamic Jihad rather than hold Hamas responsible for all violence emanating from its territory.
Israeli analysts said it was a clear signal the army sought to avoid a wider conflict in Gaza, where Israel and Palestinian militants have fought three wars since 2008.