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It came after the most serious flare-up in violence between Israel and Palestinian militants in Gaza since a 2014 war.
The intense violence that engulfed the region over the weekend began on Friday evening.
The ministry said three people, including a pregnant woman, were killed in northern Gaza and two in southern Gaza, raising an earlier toll of seven.
Israel said around 450 rockets or mortars had been fired from the Palestinian enclave run by Hamas since Saturday, and it responded with waves of air and tank strikes.
On Thursday, Israel said its aircraft struck a Hamas military compound after balloons carrying firebombs and explosives were launched across the border.
The Arab League's move comes as the Trump administration prepares to unveil a much-touted "Deal of the Century" for peace between the Palestinians and Israel in the coming months.
Scientists, who were giddy with excitement only second earlier, were visibly distraught, and celebrations at viewing centers across the country were dashed.
The victory, despite corruption allegations against the 69-year-old premier, puts him on a path to become Israel's longest-serving prime minister later this year.
Prime Minister Netanyahu, the leader of the right-wing Likud Party, is seeking a fifth term in office.
Iran is Israel's main enemy and Netanyahu spoke out strongly against the 2015 nuclear deal between Tehran and world powers.
Netanyahu visited Putin in Moscow five days before he is to seek a fifth term in office in a difficult election.
Capitalizing on internal Palestinian divisions and promoting sometimes contradictory policies, Netanyahu has succeeded in managing the conflict without addressing the bigger issue.
Israel's NSA-led delegation had reportedly left the classified documents in a restaurant. However, a waiter at the restaurant found the documents and managed to return it.