The Dutch international has arrived on a free transfer from the Cottagers, who were relegated to the Championship last season.
"John Heitinga has plenty of international experience and he is a defender who our younger players in particular will learn a lot from," said Hertha's director of sport Michael Preetz on his club's website.
Heitinga passed a medical on Monday before putting pen to paper on a two-year contract and then visiting his new home - Berlin's Olympiastadion.
"It's impressive, really impressive," the 30-year-old said after his tour of the venue for next season's Champions League final.
"I desperately wanted to move to the Bundesliga, which is why I'm really looking forward to playing for Hertha Berlin.
"I'm really looking forward to meeting the rest of the team and the great fans. After Amsterdam, Madrid and London, Berlin is now the next major capital in which I can further my career."