"I'm Still Here" was part of a hoax.
Affleck, an actor who has appeared in "Good Will Hunting," "The Assassination of Jesse James by the Coward Robert Ford" and "Gone Baby Gone," makes his directorial debut with "Here," which will soon be released in U.S. theaters.
Billed as a documentary, the film purports to be a chronicle of Phoenix's decision to quit acting and start a hip-hop career. During the past year, Phoenix has altered his appearance, gaining weight, sporting a bushy beard and dark glasses in public.
He was famously surly, uncooperative and incoherent during an appearance on "Late Show with David Letterman."
Many in the entertainment industry have speculated the double Oscar nominee has been joking but the "Gladiator" and "Walk the Line" star hasn't explained his behavior.
Affleck cleared up the mystery Thursday, telling The New York Times Phoenix's behavior wasn't real.
"It's a terrific performance; it's the performance of his career," Affleck said.
"I never intended to trick anybody," he said. "The idea of a 'hoax' never entered my mind."