The autorickshaw used for the crime has also been found, police said.
Police was on a hunt for the accused, who had abducted the student while she was returning to her room from the library in Manipal University campus and gangraped her on June 20 night.
Twelve police teams with 200 persons were working on the case.
The police had also released a sketch of one of the three accused and CCTV footage of the abduction of the victim, besides announcing Rs two lakh as reward for anyone providing information leading to their arrest. Manipal University had announced an additional Rs three lakh reward.
He said police had gathered "scientific and technical evidence" in the case. One reason for the delay in arresting the culprits was that the victim was "not cooperating and not giving statement properly to police," he said.
To prevent recurrence of such incidents, steps like installing CCTV and providing police security at university campuses would be taken, Siddaramaiah said speaking at a meet-the-press programme organised by the Bangalore Reporters Guild and Bangalore Press Club.