Sunderland's nightmare continued as they suffered their fourth defeat in five games - with the Black Cats marking new boss Alex Neil's first home game in charge by slipping out of the play-off places.
The Wearsiders have now won just one game out of nine since the turn of the year, and their slump shows no sign of slowing.
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Mo Eisa put the visitors in front just after half-time and, while Ross Stewart brought Sunderland back on terms on the hour, former Black Cat Conor Wickham scored with a quarter-of-an-hour remaining - and just minutes after coming off the bench - to give MK Dons the points.
Both Dons goals came from rapid counter-attacks, and both after January addition Jay Matete had given the ball away.
The victory meant MK Dons stay third in the table, while Sunderland slid from fourth to seventh.
Sunderland were booed off at full-time, and there were brief chants of 'you're not fit to wear the shirt' as the sense of crisis engulfing the club intensified.
Neil made two changes to the side that lined-up for his first game in charge at AFC Wimbledon last week, with Corry Evans and Leon Dajaku coming into the starting XI, with Trai Hume and Jack Clarke making way.
MK Dons boss Liam Manning made one change to the side that fought out a goalless draw against Ipswich Town last weekend, with Eisa replacing Theo Corbeanu.
Sunderland enjoyed plenty of possession in the first half, but struggled to create chances and did not test visiting keeper Jamie Cumming in the opening 45 minutes - their best effort came shortly before the break when Stewart headed wide from an Alex Pritchard corner.
MK Dons offered by far the greater threat, and Anthony Patterson made three good saves to keep the scores level.
He saved an early long-range effort from Tennai Watson, and then a couple of minutes later he was called upon again when Eisa got the better of Callum Doyle inside the area, and his shot from a tight angle was beaten away by Patterson.
But Patterson's best stop came on the half-hour when Troy Parrott found space inside the area to lash a shot at goal, but the keeper tipped the ball over the bar.
Sunderland created an opening within a minute of the second half getting under way.
Stewart burst forward in the right-hand channel and got into the box, playing a low ball across the face of goal that was just too far in front of Pritchard, who would have had a tap-in.
But Sunderland were caught out on 48 minutes, as MK Dons took the lead.
Matete was dispossessed inside the MK Dons half and Josh McEachran's played a throughball into the massive gap between Sunderland's centre-backs, releasing Eisa who outpaced Doyle and slotted his finish past Patterson.
The visitors deserved their lead, but Sunderland should have levelled almost immediately.
Pritchard won a free-kick on the left which he delivered into the box, it was headed down into the path of the unmarked Dajaku seven yard s out but he lashed his shot high and wide.
Neil made a double substitution, with Clarke and Elliot Embleton replacing Dajaku and Dan Neil.
And that switch paid dividends almost immediately as Sunderland levelled on 59 minutes.
Sunderland took a quick free-kick in the middle of the pitch and the ball was fed out to Embleton on the right, who crossed for Stewart to direct a glancing header into the left side of the net.
The Black Cats had a chance to go in front in the final 20 minutes, when Clarke got to the byline on the left but his ball into the middle was hit with such force that Stewart could not direct it on target.
And Sunderland were caught out on the counter again in the 76th minute, as Wickham made his mark on his return to the Stadium of Light.
Matete gave the ball away again in midfield and MK Dons broke forward in a two-on-one situation with Troy Parrott feeding Wickham, who had the simple task of applying the finish.
And it could have got worse in injury time, when MK Dons broke through again but this time Wickham sent his shot across the face of goal when he had only Patterson to beat.
How the teams lined up
Sunderland: Patterson, Winchester, Wright, Doyle, Cirkin, Matete, Evans (Roberts 78), Neil (Clarke 56), Dajaku (Embleton 56), Stewart, Pritchard. Subs not used: Hoffmann, Defoe, Xhemajli, Hume
Booked: Evans
MK Dons: Cumming, O'Hora, Darling, Lewington, Watson (Hayden 87), McEachran (Kasumu 62), Coventry, Harvie, Parrott, Eisa (Wickham 73), Twine. Subs not used: Ravizzoli, Smith, Corbeanu, Boateng
Booked: McEachran, Harvie
Referee: Ollie Yates (Staffordshire)
Attendance: 30,451
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