'I can't believe you haven't even seen this finished product of the new 'Bourne Identity' movie,' DeGeneres told him.
'I don't even remember making it,' said Damon.
Viewers then saw a joke preview in which the secret agent goes undercover as Lady Gaga.
Her latest single, Born This Way, is out now.
Damon's face was superimposed over the singer's body in scenes from her new music video.
'It was the diet that was the hardest part. I just remember just not being able to eat anything. And the workouts were brutal,' Damon said.
'You really commit to something. You really do,' said DeGeneres.
Later, to mark his first ever appearance on the talk show, Damon was given a special pair of boxer shorts that featured the host's face and an alarm clock.
Damon, 40, will next be seen on screen in thriller, The Adjustment Bureau.