Dubbed "Privacy Shield", the agreement replaces the 16-year-old Safe Harbour arrangement that was ruled illegal in October in the wake of the Edward Snowden revelations on US intelligence.
Businesses on both sides of the Atlantic had expressed concerns about the legal limbo and warned of the fallout if the two sides failed to reach a new agreement, which was meant to happen by the end of January.
"I'm glad to announce today that we have finalised negotiations with the United States on a renewed and safe framework for transatlantic data flows," European Justice Commissioner Vera Jourova told a press conference.
She said she expected the deal to take effect in about three months.
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In Washington, US Commerce Secretary Penny Pritzker said: "Beyond being central to transatlantic commerce, this deal also signals the closeness of the EU-US relationship."
The case stemmed from a legal challenge brought by Austrian Internet activist and law student Max Schrems against Facebook in Ireland.
Schrems sent out a series of tweets mocking the new deal, including calling Privacy Shield a "strange name," and issued a statement that the new deal could end up back in the court in Luxembourg.
But Brussels said the deal would protect Europeans.