Robin Vadakkumchery's crime only came to light after the victim gave birth to a baby in February 2017.
A child rights charity reported the delivery to the police, which led to the influential priest's arrest at Kochi airport as he attempted to board a plane to Canada.
An orphanage employee and four nuns were also accused of trying to cover up the assault but were acquitted due to a lack of evidence.
Inspector Sunil Kumar investigated the case and told the AFP: "Almost all the independent witnesses proved non-cooperative, making it difficult for us to provide substantive evidence against all that the defence threw at us."
The girl's father had told the court he was responsible for impregnating his daughter and the mother claimed the victim was older than 18 when the rape occurred.
The victim also told the court that she had been in a consensual relationship with her father while she was an adult.
However, an official doctor's record proved that the victim was a minor at the time of delivery.
Saturday's verdict followed a number of allegations against senior Church figures in Kerala, including a bishop, Franco Mulakkal, who is accused of raping a nun thirteen times over two years.
He has denied the charges.
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