"We have cracked the case by arresting Yogesh and Harish and rushed a team to nab the third suspect (Anand) who escaped to Goa," Udupi Superintendent of Police M.B. Boralingaiah told IANS.
A major educational centre, Manipal is five kilometres from the Udupi temple town on the west coast of the state and 410 km from Bangalore.
Yogesh was admitted to the Kasturba hospital for emergency treatment as he consumed poison to commit suicide after he came to know that he was about to be caught.
Police learnt from Harish that Anand fled to Goa. Harish also told them that Yogesh recorded the entire incident on his mobile phone.
The shocking incident occurred when the victim, a fourth-year 22-year-old student of the Kasturba Medical College, was waiting to hire an auto at the Manipal University campus gate to go to her flat from the library at 11.30 p.m.
Police have also traced the auto used in the crime and seized it.
A case was registered June 21 against the three culprits for abduction and rape on a complaint by the 22-year-old victim.
The heinous crime, the first of its kind in the educational centre, sparked off protests by students of the six-decade old privately-run university.
Police formed eight teams and announced a Rs.2 lakh cash reward for vital information that could lead to the accused.
"We will investigate the case under the new anti-rape law and see that they spend their rest of life in jail," Additional Director General of Police Bipin Gopalakrishna said.