The breakthrough ruling is the first civil court judgment against the majority Roman Catholic church in Argentina, legal experts said.
The court issued the judgment of 756,000 pesos against the church in the case of a theology student in the province of Santa Fe, who claimed to have been victimized by late Archbishop Edgardo Storni.
Seminary student Ruben Descalzo filed a lawsuit claiming he was sexually assaulted by Storni in 1992.
A court in 2009 found Storni guilty of the sex assault charges against him and sentenced him to eight years in prison, but the sentence was overturned two years later by an appeals court.
The sentence was sent back to the lower court which was instructed to issue a new sentence against Storni, who died before the court could act.
Storni died in 2012, at the age of 75 without ever confessing to the crime he was accused of.
He gave up his position in 2002, and secluded himself at a property owned by the archdiocese.
Saturday's court ruling ordered the court to make payment of the fine within the next 10 days.
It was not immediately known whether the church planned to file an appeal.