MK Dons are without a win in 10 at Stadium MK after Bury's smash-and-grab win on Tuesday night.
James Vaughan opened the scoring with a brilliant volley after eight minutes before Dons got their act together, peppering Ben Williams' goal with shots.
After hitting both posts, Ben Reeves finally converted to equalise but parity would last just five minutes as Vaughan poked home Bury's second.
Committing David Martin forward for a stoppage time corner, former Dons loanee Zeli Ismail broke to score their third.
READ MORE: REPORT: MK Dons 1-3 Bury