Kismat Ali and Mohammad Garib, both 21 years old, were held from Uttar Pradesh's Amethi and Faizabad districts respectively. The auto driver, Mohd Irfan (29), was arrested on Friday.
They had together planned to commit the crime. The victim identified Ali and Garib in a test-identification parade today, police said in a release.
Police said the arrested duo, who work as labourers, knew each other. Both had come to Zirakpur in Punjab, near here, with their parents about five years ago.
She had taken the auto rickshaw after attending a stenography class from sector 37 here. Ali and Garib were already sitting in the auto, according to a complaint filed by the woman, the police had said earlier.
The auto-rickshaw driver allegedly drove her to an isolated place in Sector 53 here, instead of taking her to Mohali where she had been staying as a paying guest, they had said.
The three men dumped the victim in Sector 53 after allegedly raping her, police had said.