De la Fuente, 19, has agreed a four-year deal with Marseille, who are owned by American businessman Frank McCourt, the former owner of the Los Angeles Dodgers.
Barca will be due 50% of any future transfer fee, sources have told ESPN. The Catalan club had hoped to add a clause to re-sign De La Fuente within a certain timeframe but regulations in French football did not allow one to be included.
ESPN first reported in April that Barca were willing to listen to offers for De La Fuente this summer, with interest coming from Spain, Germany and France.
He featured prominently for the B team in the second half of the campaign, helping them reach the playoffs in the third tier of Spanish football, but told ESPN it had been difficult alternating between the two teams.
ESPN revealed last week that Marseille had emerged as the frontrunner to sign him.
Coach Jorge Sampaoli even phoned De La Fuente, who has been at Barca since 2013, to explain how he will fit into his plans at the French club and what his role would be.
De la Fuente has been capped by the U.S at Under-16, U18 and U20 level and received his first senior call-up last November, playing 71 minutes in a goalless draw against Wales.