However, Palestinian officials said a ceasefire had now been agreed thanks to "Egyptian and global efforts".
Israeli military spokesman Lieutenant Jonathan Conricus said the goal of Saturday's operation was to stop arson attacks, attempted border breaches, and assaults on soldiers from Gaza that have grown increasingly violent.
But no blame was cast on Israel and police said they had launched an investigation into the cause of the blast.
The protest organisers say the demonstrations aim to press demands such as for a right to lands lost to Israel in the 1948 war of its foundation and for an Israeli-Egyptian blockade to ease.
Gaza health officials say more than 130 Palestinians were killed and 15,000 others injured by Israeli forces during the protests.
The Israeli army said it carried out the strikes on Saturday, with its fighter jets targeting "complexes used to prepare arson terror attacks and a Hamas terror training facility".
Gen. Ronen Manelis, the operation had three aims: To end the incendiary kites and balloons from Gaza, end the large-scale border protests, and end the rocket and mortar fire.
According to Israel Radio, residents reported hearing sounds of explosions and possible interceptions by Israel's Iron Dome system.
United States envoy hails North Atlantic Treaty Organisation squeeze
Trump's comments prompted both the House and Senate to introduce non-binding resolutions affirming US support for the alliance. But experts say the United States can not force any allies into spending more , no matter how much the president balks.
Israel launched the first airstrikes early Saturday after an IDF officer was injured by a grenade thrown at him during a violent riot along the Gaza border on Friday.
Israeli warplanes targeted an under-construction building in al-Katiba neighborhood in Gaza on Saturday, the Palestinian Health Ministry said.
Damage caused to the back yard of a house that was hit by a rocket from Gaza in the southern Israeli city of Sderot, on July 14, 2018.
In Israel, air raid sirens sent people rushing to shelters in areas surrounding the Gaza Strip as rockets and mortars were fired from the Palestinian enclave at nearby communities.
"The focus of the attack is a wide-scale strike of the Hamas Battalion HQ in Beit Lahia, which includes urban warfare training facilities, weapon storage warehouse, training compounds, command centers, offices and more", the IDF said in a statement.
The Israeli military last reported fire from Gaza around 1:30 a.m., and said special orders put in place in southern Israel over the weekend, including a prohibition on large gatherings, had been lifted.
The Israeli army killed two Palestinians, including a teenage boy, and wounded hundreds at protests along the fence with Israel on Friday.
The majority were involved in protests and clashes but others were seeking to breach or damage the border fence. It said 70 others were wounded, at least 20 by live fire, and others by tear gas.
Israel and Egypt say the blockade is a necessary security measure against militants.