Mark Robins' men, buoyed by their first league win of the season at Oldham on Saturday, started very strongly and could easily have been in front in the early stages.
David McGoldrick picked out Carl Baker with a far-post cross in only the third minute but his volley was well pushed aside by David Martin.
The home side were also slightly unlucky not to win a penalty three minutes later when Darren Potter appeared to handball right in front of the referee inside his own area.
The visitors, who started in third place, hit back when Charlie MacDonald picked a loose ball from Richard Wood only for William Edjenguele to get back and clear in the nick of time.
Wood made up for it in the 34th minute when he leapt to meet a corner from Gary McSheffrey and head powerfully home. But they could not keep hold of their lead and MK Dons were level in the 42nd minute when a shot from Stephen Gleeson hit Edjenguele and deflected in.
