"He actually looked you in the eye and said he put victims first. How dare he?" the prosecutor asked jurors during his more than 2½-hour closing argument.
Lynn's conspiracy count related to an allegation that he schemed with Avery and other archdiocese officials to endanger children.
Avery had been due to go on trial with Brennan and Lynn, but he pleaded guilty in March to a sexual assault that occurred during the 1998-99 school year.
The 69-year-old was sentenced to 2½ to five years in prison.
Brennan himself was removed from the active ministry in 2006. Two years later, he admitted that he had allowed the youngster to view pornography and sleep in the same bed with him in 1996, according to church investigators' testimony.