Roberto Di Matteo's side recovered from conceding an early goal to chalk up their seventh victory on their travels.
Brighton are in contrastingly poor shape. This was their fifth defeat out of six in all competitions and victory for Yeovil at home to Stockport on Saturday will drop the Seagulls into the relegation zone.
That seemed improbable when Bradley Johnson gave the South Coast strugglers a second-minute lead.
The midfielder on loan from Leeds latched on to a quickly taken free-kick by Glenn Murray to lift the ball over advancing goalkeeper Willy Gueret.
The visitors responded strongly and they were level in the 27th minute. Spanish centre-half Miguel Angel Llera, returning from suspension, rose highest at the far post from a corner to head home through a crowd of players.
Aaron Wilbraham was denied by a post on the stroke of half-time but MK Dons did not have to wait long to get their noses in front.
Jemal Johnson rifled in an angled left-foot drive seconds after the restart to rock Brighton and they fell further behind in the 69th minute.
A bad mistake by young centre-half Tommy Elphick, who failed to deal with a high ball, allowed Peter Leven to tuck away his seventh goal of the campaign.
That added insult to injury for Brighton, as they had two bids for the Scottish midfielder turned down by his previous club, Chesterfield, during the January transfer window.
Substitute Stuart Fleetwood gave the home side fleeting hope with a well-struck volley two minutes from time.
It proved short-lived however, as Jason Puncheon scored a superb solo effort, dancing his way past a couple of Brighton defenders in the first minute of stoppage time, to complete an eye-catching victory for Di Matteo's men.