The Premier League Cup match held at Leek Town's Harrison Park ended 0-0.
But in the final minute Blues were sure they should have had a penalty when Steve Seddon was clipped by a defender.
Nonetheless, Blues, after recently shipping too many goals, shored things up considerably to frustrate their hosts.
Coach Richard Beale altered the side's shape to include wing-backs and a midfield diamond four.
Beryly Lubala led the line up top with Wes McDonald in behind, at the point of the diamond.
"Since Gianfranco Zola has come in we have mirrored what the First Team have done," said Beale, Blues Senior Professional Development Coach.
"But I felt we had to be more pragmatic after recent results and the gaffer was all for it.
"The foremost aim was to keep a clean sheet and that's what we did. We had a very young team out, but the lads did what was asked of them and the biggest compliment is that Stoke changed their shape at half-time to mirror ours.
"They struggled to break us down and we were very lively on the break.
"How we didn't get a penalty at the end I don't know. Steve Seddon's first touch has taken him past a defender, who then clips his back legs. He stumbled and got a cross in, which was cleared. Had he gone down maybe the referee would have given it, but he should have done anyway."
Wes Harding in particular impressed Beale. Harding was the right side of the three centre-halves.
"Wes gave a captain's performance," said Beale. "He looked like a First Team pro in terms of his decision making, when to go to attack the ball or drop, helping balls down the side or in behind.
"Wes McDonald, too, I was pleased with. In the last three or four months Wes has really twigged that you have to work really hard without the ball as well. He's added that to getting his shots away, creating things and causing danger."
The result means Blues have an outside chance of qualifying for the knockout stages of the competition from Group H with one match left to play.
Blues: Weaver, McCoy, Seddon, Baba, Harding, Kwiecien, Arthur (Bailey, 69), Mulders, Lubala, MacDonald, Lakin. Not used: Timms, Siviter, Bajrami.