Chulalongkorn University expressed its "deep regret" over the painting, which appeared last week and featured Superman, Batman and the Incredible Hulk as well as Hitler.
In a letter to the Simon Wiesenthal Center, which had complained about the poster, the university said the students who created it were "unaware of its significance" and had been warned.
A picture posted on the Simon Wiesenthal Center website shows a young woman in a graduation gown giving a Nazi salute in front of the giant mural, which reads "Congratulation".
"The painting, which has now become a topic of debate, is not intended to refer to anyone particularly," the University said.