The 41-year-old actor will replace Christian Bale as 'the caped crusader', becoming the eighth actor to play the part. Other luminaries include George Clooney and Michael Keaton.
Oscar-winner Ben will make his debut in the 2015 film opposite British actor Henry Cavill, who will reprise his role as Superman from the most recent film, Man of Steel.
It will the first time the two superheroes have been brought together on film.
"We knew we needed an extraordinary actor to take on one of DC Comics' most enduringly popular super heroes, and Ben Affleck certainly fits that bill and then some," Warner Bros President Greg Silverman said in a statement.
Director Zack Snyder said Ben will provide an "interesting counter-balance" to 31-year-old Henry's Clark Kent.
"(Ben) has the acting chops to create a layered portrayal of a man who is older and wiser then Clark Kent and bears the scars of a seasoned crime fighter, but retain the charm that the world sees in billionaire Bruce," said Zack, who also directed Man Of Steel. "I can't wait to work with him."
The sequel — currently untitled — will reunite Man of Steel stars Amy Adam (Louis Lane), Laurence Fishburne (Perry White) and Diane Lane (Martha Kent).
It's not the first time that dad-of-three Ben has ventured into the Superhero genre; he starred as blind vigilante Matt Murdock in the 2003 film Daredevil.