Police said the woman took the private bus from Dewas, around 40 km from Indore. On entering the city, all passengers except her got off at Vijay Nagar.
The driver then took the bus to near a flyover, where another man boarded. The two and the bus conductor allegedly gang-raped the woman.
The woman's medical report has confirmed rape. The three suspects have been arrested and the bus impounded.
Police said the bus, which has been impounded, had tinted windows despite a recent crackdown against such vehicles in Madhya Pradesh.
The drive to penalise public transport buses having tinted glasses was started after last December's gang-rape of a medical student on a Delhi bus, but stopped after protests by bus operators.