Phoenix stunned viewers during an interview on Letterman's talkshow last year, in which the unkempt actor, sporting dark shades, slurred his words and mumbled monosyllabic answers.
Appearing on the show for the first time since the incident, Phoenix told Letterman that he was sorry for his behaviour, which was since confirmed to be an act for his mock documentary I'm Still Here.
Phoenix told the host on Wednesday's Late Show: "I think that you've interviewed many, many people, and I assumed that you would know the difference between a character and a real person - but I apologise. I hope I didn't offend you in any way."
"Oh no. Oh no, no, no," Letterman replied. "I'm telling you, it was so much fun. It was batting practice, you know what I mean? Every one of them was a dinger."
The comedian also denied suggestions that he was in on the hoax.
"Was there a script that you and I were working with?" he asked Phoenix, to which the actor responded: "No. We'd hoped to come on a talkshow, and I was looking for a beat down, and I got one... I want to thank you for that."