A superb solo goal by Benik Afobe proved to be the difference as the Dons ran out 1-0 winners at the Proact Stadium.
Daniel Powell and Afobe replaced Danny Green (hamstring) and Will Grigg, who dropped to the bench, for the clash with the Spireites.
The Dons were the first to really threaten four minutes in when Lee Hodson set Afobe away down the right-hand side but, after making good yards, the striker was denied by a smart save from Tommy Lee.
Ben Reeves then saw a shot well blocked 60 seconds later after good work by Powell down the opposite flank as Karl Robinson’s men started on the frontfoot.
The hosts soon warmed up, though, and David Martin had to be alert to gather Samy Morsy’s shot from the edge of the box 13 minutes in.
As the exciting opening continued, the men from MK1 broke down the right but Bowditch nor Reeves could turn home Hodson’s teasing cross.
At the other end, centre-backs Kyle McFadzean and Antony Kay had to be on their metal to block Gary Roberts’ effort and clear a dangerous delivery respectively as the midway point of the first half approached.
Morsy tested Martin once again on 26 minutes with a stinging 30-yard drive which was dealt well with by the Dons keeper.
The Spireites went even closer shortly afterwards with McFadzean forced to clear Evatt’s header off the line before the returned cross was directed against the post by Sam Hird.
Robinson’s men almost caught Chesterfield cold with just over 10 minutes of the first half to play but Afobe fired his 15-yard volley over the top after being expertly found by Bowditch.
An earlier challenge from Roberts forced Martin off at half-time, with Ian McLoughlin replacing him in the Dons goal.
A mix-up between McFadzean and Kay presented Eoin Doyle with a golden opportunity to give the hosts the lead in the first minute of the second period but he curled his effort wide of when well placed.
Afobe was more clinical three minutes later, though, when he picked the ball up, drove at the Spireites’ defence and fired an unstoppable effort past Lee from the edge of the area to give the visitors the lead.
The Dons were dealt a further injury blow shortly afterwards when Hodson had to be stretchered off, with George Baldock replacing him at right-back.
As the clock ticked towards the hour mark, referee Drysdale waved away what seemed to be strong penalty appeals when Powell appeared to be brought down by Lee inside the area.
The Dons came so close to making it 2-0 on 66 minutes when goalscorer Afobe’s clever reverse pass found Baldock, whose teasing cross just eluded Reeves as the visitors broke with pace and purpose.
It really should have been a two-goal advantage four minutes later when an inch-perfect pass from Reeves picked out Afobe, but the striker appeared to mis-judge it at the back post and the chance went begging.
A superb run from Alli, who left three defenders in his wake, gave Afobe another chance with 15 minutes remaining although his low drive deflected into the grateful arms of Lee.
Chesterfield continued to pose a threat at the other end, however, they were struggling to find a way past an extremely solid Dons defence.
A quick break in the final minute of normal time almost completed an impressive away-day display, particularly the second half, but substitute Will Grigg, on for Bowditch, saw his shot deflect wide after more good work by match-winner Afobe.
Ian Evatt headed over the hosts’ best chance of a reasonably comfortable stoppage time for the Dons, who ultimately deserved their second win of the season against a dangerous Chesterfield side.
Starting XI: Martin (McLoughlin 46); Hodson (Baldock 54), Lewington (c), Kay, McFadzean; Alli, Potter; Powell, Reeves, Bowditch (Grigg 89); Afobe.
Unused subs: Burns, Flanagan, Randall, Hitchcock.
Goals: Afobe (49).
Bookings: McFadzean, Reeves, Baldock.
Attendance: 5,811 (246 Dons fans)