The sniper is the only person to face prosecution over the killing of civilians during the three-week Israeli incursion launched at the end of 2008.
Investigators said they had uncovered evidence that the soldier identified as "First Sergeant S" opened fire as the victims walked with a group of people waving a white flag.
The charge comes as international pressure continues to charge certain officials and soldiers with war crimes for their roles in the operation.
Such cases could be deeply embarrassing for Israel and have made it difficult for some of its most senior politicians and army officers to travel outside of the country for fear of arrest.
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