Cammy Smith and Jordon Brown were the goalscorers in a game that manager Craig Brown was pleased with but felt that the result perhaps masked an indifferent overall performance.
Boss Brown told RedWeb: "We cannot be totally pleased with the way we played, we can be pleased with the result and the goals we scored but we gave too much possession and territorial possession to the opposition.
"However I cannot complain because we left our first team at home."
Seven of the starting XI were products of the Dons youth system, and as such it was an excellent result against a good European club.
The Dons took the lead on 81 minutes when 17-year-old Smith fired home from outside the penalty box.
Jordan Brown added a second on 85 minutes when he followed up a Michael Paton shot to tap in.
Manager Brown added: "Cammy is particularly outstanding.
"He has now just turned 17 and I think he is going to be a wonderful player.
"It was an excellent strike and also excellent control just before the goal."