The accident occurred near Gujaluru in Chivvemla mandal of Nalgonda district.
A private bus coming to Hyderabad from Vijyawada hit the three-wheeler from behind.
Three women travelling in the auto-rickshaw were killed and six others were injured.
They were returning to their village after prayers at a church in Suryapet town in the same district.
Police said while two women died on the spot, the third succumbed at Suryapet Area Hospital. The condition of two of the injured is stated to be critical.