Town came from behind to book a place in the next round of the Capital One Cup thanks to a debut goal from Josh Yorwerth and the winner from Jay Tabb.
Stevenage led just past the half hour when Christophe Berra unluckily diverted the ball into own net after Dean Gerken had saved from Dean Parrett.
Yorwerth headed Blues level early in the second-half and Tabb won it for Blues 13 minutes from time after David McGoldrick had set him up.
Stevenage were seemingly handed a lifeline late on when Berra was judged to have fouled Parrett in the box but referee Fred Graham changed his mind, much to the obvious anger of Boro boss Teddy Sheringham.
Only skipper Luke Chambers remained from the starting line-up against Brentford at the weekend, with Town fielding four debutants, Larsen Toure, Brett Pitman and youngsters Myles Kenlock and Yorwerth.
Pitman sent a volley just wide at the near post after finding a few inches of space, Charlie Lee seeing a shot deflected for the visitors, with Steven Schumacher then sending a 25 yarder just wide.
Parrett’s shot was deflected to safety by Berra, then Kenlock did even better to divert Fraser Franks’ header away for a corner as the League Two side enjoyed the better of the opening exchanges.
David McAllister then lashed a shot wide of Gerken’s goal from a great position after Dipo Akinyemi had set him up as the visitors continued to look the more likely to open the scoring.
Chambers was wayward with his cross after Jonathan Douglas released him down the right as Town looked to get a foothold in the game but it was Sheringham’s team who went ahead on 33 minutes, Parrett’s shot was saved by Gerken after Akinyemi’s run but the ball cannoned back off the unfortunate Berra and into the net.
Town were almost level immediately with a great touch and then 50 yard pass from McGoldrick finding Pitman who raced inside the box but was inches away from burying his shot into the far corner.
The goal seemed to sting Blues into action and an excellent pass from Kenlock found Tabb in the box but Chris Day did enough to keep Boro’s lead intact through to the break.
Ryan Fraser was introduced as a half-time substitute, Toure, who picked up an injury in the latter stages of the first 45 minutes, making way.
Yorwerth couldn’t keep his shot down after his header from a corner had fallen back into his path, then Pitman showed a lovely touch to get away from his marker and set up Tabb whose cross was deflected wide.
Town were level from the flag kick though, Fraser’s delivery was met by Yorwerth’s firm header on 55 minutes.
Kenlock fizzed a cross just in front of the supporting Tabb at the far post as Town looked far more of an attacking threat, Pitman then denied by Day’s outstretched hand from Fraser’s cross.
Day reacted well to keep out McGoldrick’s header from Fraser’s corner, Fraser hitting the sidenetting with a left footer, the Scotsman’s introduction at the break giving Blues real pace down the flanks.
It was Fraser who again provided the ammunition for Chambers at the back post, his header just wide before Town got the goal the play had been threatening on 77 minutes, Tabb sliding the ball into the net from McGoldrick’s set up after Douglas’ clever pass over the top.
Stevenage were awarded a penalty seven minutes from time when Parrett went down under Berra’s challenge, the referee initially awarding the spot-kick then changing his mind after talking to his assistant, who appeared to give the decision in the first place. Bizarre!
Tabb and McGoldrick went close to grabbing a third as Town won a cup game for the first time under Mick McCarthy.