The male student, then aged 20, at Otemon Gakuin University in Osaka prefecture, jumped from a building three years ago, leaving a note saying, "The bullying I keep getting at school...Cannot take it any more."
The student, who was born to Indian parents and grew up in Japan, had earned Japanese citizenship, a university official said.
Compounding the tragedy, his father, depressed about his son's suicide, later jumped to his death from the same building, according to local reports.
"I would like to express my heartfelt apology to the bereaved family members," said university dean Masayuki Ochiai at a press conference.
The university refused to comment on whether the abuse was racially motivated saying the specific nature of the bullying was not known.
Local media said he had been forced to take his trousers down in front of other people and that he had been nicknamed "bin Laden".
An independent third party panel was created in October to probe the incident after the Sankei newspaper and public broadcaster NHK reported the case.
Japan, a country where more than 30,000 people commit suicide every year, often sees school children kill themselves, with many leaving notes referring to harsh bullying by their peers.