Andrew Gilmour, 76, from Glasgow, denied committing the offences at locations in Glasgow and the Western Isles between 1989 and 1995.
He was convicted at the High Court in Glasgow after the victims, now aged 35 and 40, gave evidence against him.
The court heard that Gilmour abused his victims when they were aged 11 to 15 and 13 to 14.
Jailing him, judge Lord Bonomy told Gilmour: "You were in a position of very important trust.
"To do justice in this case it is necessary to impose a prison sentence."
Gilmour was also placed on the sex offenders register.
One victim, now aged 35, told the court that he was touched inappropriately by Gilmour in a church and church hall in Glasgow, as well as Gilmour's home.
He said: "What was happening was absolutely wrong. I was scared and felt confused."
The victim told the court that he decided to come forward after seeing a woman, who was abused as a child, telling of her experience on television.
The man broke down as he told the jurors: "The woman said during her interview: 'If nothing else I can stop it happening to anyone else'.
"As I watched I felt disgusted with myself that I could have left there and let it carry on with someone else and not done anything about it."
He was asked if he was sexually abused in the church and replied: "Yes, one of the places was a room in the church where the minister would get ready."
The victim added: "He would also touch me inappropriately when I was helping him set out the Bibles in the church."
He also told of how he was abused in a church in the Western Isles during a Boys' Brigade camp.
A former Boys' Brigade captain has been jailed for two years for sexually abusing two boys in his company.