The defender has agreed a two-year contract with the Bundesliga side after passing a medical earlier today.
The Dutch international told the German league's website: "I was desperate to play in the Bundesliga, that's why I'm really looking forward to playing for Hertha. I'm looking forward to meeting the team and their terrific fans."
The club's sporting director Michael Preetz added: "John Heitinga is a defender with international experience, from whom our younger players in particular will learn a lot."
Heitinga, who joined Fulham from Everton last summer, made 14 appearances for the Cottagers last season.