Town’s exit from the competition had already been confirmed before this game but they were involved in an entertaining contest at Stadium MK as Charlie Waller and Darragh Burns cancelled out Manny Monthe’s first half header before Tyreece Simpson made it 2-2 from the penalty spot.
But Dons would take the spoils and secure top spot in Southern Group F thanks to Dawson Devoy’s fantastic late strike.
Captain Jon Guthrie returned from seven weeks out to start and teenage academy prospect Rueben Wyatt lined up alongside Ryan Haynes in midfield as all 10 outfield players who started against Burton Albion last time out were rested.
The bench was made up entirely of players who have come through the club’s academy, including fit-again Max Dyche.
Haynes had an early shot easily held by Michael Kelly while Will Hondermarck’s half volley deflected over but both teams were predictably disjointed in a dreary first half that closer resembled a pre-season friendly than a competitive fixture, although Jon Brady did manage to get himself booked and potentially suspended for the weekend.
Guthrie and Louis Appéré were scheduled to play 30 minutes apiece and both men came through unscathed before being taken off just beyond that mark, replaced by Max Dyche and Neo Dobson.
Northampton led a few minutes later when Ali Koiki, now wearing the armband, hurried down the left flank and won a corner, from which Monthé rose highest to head in after an excellent delivery by young Wyatt.
That was a rare moment of excitement and the next bit of action didn’t come until first half stoppage-time when Kelly was at full stretch to tip Simpson’s curling effort around the post.
Haynes was close to scoring a fine solo effort shortly after the break, whizzing a low shot just wide after winning the ball back himself, before MK Dons went up the other end and levelled through Waller’s deflected shot.
The hosts turned things around 10 minutes later when Cobblers didn’t deal with a long ball and Matthew Dennis slipped in Burns who rifled a powerful shot into the roof of the net.
Max Thompson prevented Brooklyn Ilunga from extending Dons’ lead, and that meant Cobblers were able level things up nine minutes from full-time when Simpson sent Kelly the wrong way after Wyatt was tripped in the box.
But Town were on level of terms for just a matter of seconds as MK Dons scored what proved to be the winner, Devoy picking out the top corner with a terrific strike from 25 yards.
MK Dons: Kelly, Lewington © (Stirland 66), Ilunga, Burns, Anker (Silver 66), Stewart, Devoy, Dennis (Medwynter 84), Waller, Wood, Lewis-Burgess (Clark-Anderson 78). Subs not used: Bedford, Boyce, Daffern
Cobblers: Thompson, Odimayo, Guthrie © (Dyche 34), Monthé, Lintott, Koiki (Scott 73), Haynes, Wyatt (Cartwright 90), Hondermarck, Appéré (Dobson 34), Simpson. Subs not used: Dadge, Ireland, Hart
Referee: Sam Purkiss