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.
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
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