Saints' youngsters were unfortunate to come away from the Midlands defeated on Saturday morning.
The Under-18's controlled most of the play but could not make their possession tell as the Blues snatched two goals inside the last half an hour.
The hosts took the lead on 60 minutes when a cross found its way into the area and was subsequently turned home to put Birmingham in front.
Saints continued with their endeavor but were cruelly undone in the last minute, as a swift counter-attack from the Blues sealed the win.
Youth Team Coach Dave Puckett felt that the score line was not a true reflection of the game.
"We played at a decent tempo and were particularly good in midfield and out wide but we didn't trouble them with enough shots," he said.
"It's a disappointing result when you consider how much of the play we had. However, we can take heart from some good individual and team performances. Unfortunately we were punished by a good side and we will have to learn the lessons from that."
Saints Under-18's: Dovey, Martin, Harper, Tafazolli, Argent, McLean, Robinson, McNish, Preen (Oxlade-Chamberlain 80), Garrod (Keegan 30), Hoskins.
*After the game, winger Garyn Preen who had been on standby for the Wales Under-19's, was called up by coach Brian Flynn and will now join teammate Ryan Doble in Malta next week.