During the convocation ceremony, when Mr Sunkanna's name was called, he came to the stage but refused to take the certificate from Mr Podile. Then, Pro-Vice Chancellor Vipin Srivastava came forward and handed over the PhD degree to Mr Sunkanna.
Mr Sunkanna and Mr Vemula were among the five students, who were suspended from the university hostel last year on "disciplinary" grounds. Their suspension was later revoked.
In January this year, Mr Vemula's body was found hanging in a hostel room at the university campus. The Dalit scholar's suicide caused an outrage and triggered widespread protests with the university students seeking Mr Podile's ouster.
"I refused to take my certificate from him in protest (over the VC's alleged role in the Vemula suicide case)," Mr Sunkanna, who is currently doing his post-doctoral course in Philosophy from IIT Bombay said.
When contacted, Mr Podile downplayed the incident, saying it is a student's choice whether or not to accept certificate from him.
"That is his choice. Let us not worry too much about that (Sunkanna's refusal)," he said.