Trailing to a 29th minute goal by Jacob Brown, Blues' most threatening moments came late on.
With only five minutes left, Viv Solomon-Otabor burst into the box, breezed inside one challenge and saw his low shot kept out by former Blues 'keeper Nick Townsend.
And then in stoppage-time, Solomon-Otabor then embarked on a dribble through the middle before cracking a bouncing attempt that just nipped past the post.
In truth, Barnsley could have made it safe by then on the counter attack as Blues tried for all their worth to get the equaliser.
But Blues were also fuming at a 77th minute decision that went against them: from a diagonal cross into the box by Luke Maxwell, Callum Evans shoved Daniel Cleary in the back as he rose to nod the ball down.
It seemed for all the world a penalty but the referee was having none of it.
The introduction of Wes McDonald helped perk up Blues, who were not always able to get much joy out of a well-drilled Barnsley rearguard.
Reece Brown had a couple of pot-shots from distance for Blues in either half but Townsend was not overly-exerted, until more intense pressure came towards the end.
Corey O'Keeffe performed well, raiding forcefully down the right, but Blues could never quite find a finishing edge in and around the box when it mattered.
At the beginning of the match a Reece Brown free-kick was well met by Josh Martin and his header towards the bottom corner was tipped round the post by Townsend.
But Barnsley, under the charge of former Blues Professional Development Coach Paul Harsley, made the breakthrough with what proved to be the decisive goal just before the half-hour mark.
Jake Charles broke into the Blues box and although Jake Weaver made an initial save from his shot, Jacob Brown was on hand to steer the loose ball over the line, just out of reach of Steve Seddon.
Blues: Weaver, Cogley (McDonald 59), Seddon, Maxwell, Cleary, Martin, O'Keeffe, Baba (Popa 72), Storer, Brown, Solomon-Otabor. Not used: Trueman, McCoy, Mulders.