The pair, 19 year old Dinesh Dhurv and 25 year old Jitendra Pathak, were charged after a 48 year old women claimed two masked men forced their way into her room and tied her hands and feet before gang-raping her.
The victim was attacked at the Krist Sahaya Kendra centre - which treats children and people with minor injuries - in Raipur, the capital city of the central state of Chhattisgarh on 19th June 2015.
Judge Nidhi Sharma a judge at a fast track court in Chhattisgarh has ruled there is not enough evidence to convicted Dhurv and Pathak over the incident.
According to the Times of India, police and other authorities initially tried to downplay the attack and avoided mentioning that the rape survivor was a nun.
Officers later interrogated more than 200 people in order to find the attackers amid mounting protests over their handling of the attack.
The nun, who is originally from the southern Indian state of Kerala - which has a significant Christian population - belongs to the Salesian Missionaries of Mary Immaculate.
The attack was condemned at the time by state Congress and the Chhattisgarh Christian Forum as a "systematic attack on minorities in the state".
The Catholic Bishops' Conference of India had raised fears that such incidents highlight concerns questions on the safety of minorities living in India.