Scott Muirhead, Richard Foster and Stephen Tarditi all missed presentable opportunities and the youngsters were made to pay when Dundee took a first half lead.
Playing with the wind in the second period, the Pittodrie babes continued to dominate proceedings but were caught on the counter attack as the Dark Blues doubled their advantage.
Tarditi finally found the net with five minutes remaining to give the Dons hope and they almost snatched an equaliser right at the death but the Dundee keeper made a superb save to deny Zander Diamond's header.
Drew Jarvie was left to wonder how his team had failed to win. "We created so many chances, I find it hard to believe we lost. We deserved something from the game, but if you don't score when the opportunities are there you pay the price."