Rafferty, Chestnut Grove, Newry, who pleaded guilty at Craigavon Crown Court to four counts of indecent assault when the girl was 16 and he was 38, was also given a three-year probation order.
He was banned from working with children or vulnerable adults for 10 years.
After the judgment, Kate Walmsley, chairwoman of Survivors and Victims of Institutional Abuse, called for the Northern Executive to establish a public inquiry into all cases of clerical child abuse.
The Executive's inquiry into institutional child abuse does not take in clerical child abuse.
"This is just the latest in a long line of cases of clerical abuse where victims have been let down by the authorities," Ms Walmsley said. "Our abuse cases are not covered by the institutional abuse inquiry now under way, but we too deserve the truth. The Executive must hear our call for justice."