The League One side took the lead just three minutes into the game with Jermain Easter scoring from the penalty spot after Craig Gardner was adjudged to have handled a Luke Chadwick cross into the box.
Just five minutes later James McFadden had the perfect opportunity to level for Blues. Gardner was fouled in the Dons' penalty box but McFadden hit the post from the resulting spot kick.
Moments later Nikola Zigic did have the ball in the net but the goal was ruled out after the referee's assistant adjudged Seb Larsson's cross to have gone out before reaching the Blues striker.
The Dons came close to taking a two-goal lead on 25 minutes but Ben Foster came to Blues' rescue when saving well with his legs from Easter's close range shot.
Lee Bowyer had a great chance to equalise for Blues eight minutes before half time. Zigic's flick-on found Larsson out on the right wing and his cross was met by Bowyer at the back post but the Blues midfielder shot into the side netting when he really should have found the back of the net.
Scott Dann also went close with a header from a Larsson corner as the first half drew to a close.
Early into the second period half-time substitute Garry O'Connor hit the post with a header from another Larsson corner.
The hosts broke quickly from the defensive clearance, however, and took a 2-0 lead through Jabo Ibehre.
Blues reduced the deficit on 53 minutes when another of Alex McLeish's half time substitutes, Cameron Jerome, latched onto a Barry Ferguson through ball and sidefooted a right footed shot wide of the Dons' keeper David Martin.
Jerome scored his and Blues' second goal of the evening on 77 minutes with a sweet left footed shot from the edge of the box.
In-form striker O'Connor scored what proved to be the winning goal when his left-footed shot from 18 yards out found the back of the net via a deflection off an MK Dons defender two minutes from the end of normal time.
Blues: Foster, Parnaby (Fahey, 35), Johnson (Ridgewell, h/t), Dann, Murphy (Valles, 60), Larsson, Gardner (Mutch, 65), Ferguson (Michel, 60), Bowyer (O'Connor, h/t), McFadden (Phiilips, 75), Zigic (Jerome, h/t).
Referee: Andy Woolmer
Attendance: 5,869
The pre-season schedule continues on Wednesday night when a BluesXI take on Solihull Moors at Damson Park before the only home friendly of the summer against Spanish outfit Real Mallorca take's place at St Andrews on Saturday afternoon.