The nun was raped by a Hindu mob in Kandhamal district, days after riots between Hindus and Christian there.
Riots began after a Hindu religious leader was shot dead.
Although left-wing Maoist rebels in the state claimed responsibility for the killing, hard-line Hindu groups blamed the minority Christian community for the death.
More than 30 people were killed in the violence and dozens of churches and Christian institutions were vandalised.
Police had arrested nine people in connection with the rape of the nun. One accused is still being sought.
On Friday, Judge Gyana Ranjan Purohit found Santosh Patnaik guilty of rape, and Gajendra Digal and Saroj Badhei guilty of molestation.
Patnaik was sentenced to 11 years in prison, while Digal and Badhei were each sent to prison for 26 months.
Six of the other accused were acquitted by the court in Orissa because of lack of evidence.
The Catholic nun, working with the Divyajyoti Pastoral Centre at Kanjemandi village, alleged that she was dragged out of a Hindu man's house where she had taken shelter along with a 55-year-old priest, Father Thomas Chellantharayil.
She was taken to an abandoned house where she was raped by a mob on 25 August 2008. She also alleged that she was paraded naked through the streets.
Hindu groups in Kandhamal had accused Christian priests of bribing poor tribes and low-caste Hindus to convert to Christianity.
Christians said lower-caste Hindus converted willingly to escape the Hindu caste system.
A court in India has found three people guilty in connection with the rape of a Catholic nun in Orissa state in 2008.