Roberto Di Matteo's men had gone four games without a victory before the game, a run which all but ended their chances of automatic promotion to the Championship.
But Ali Gerba's ninth goal of the season coupled with a rare Jason Puncheon header handed Dons the three points against an injury-ravaged Brighton side.
Brighton came closest to opening the scoring in the early stages when Craig Davies found Lloyd Owusu in the box but Dons' goalkeeper Willy Gueret pulled off a superb double save from close range.
Dons then made the breakthrough after 29 minutes as Gerba picked up a Sam Baldock pass and found the bottom corner of Michel Kuipers' goal before Brighton's frail defence was breached again 11 minutes later when Puncheon headed home Mark Wright's cross.
Owusu remained the Seagulls' biggest threat after the break and he set up Dean Cox to shoot just wide in a rare Brighton venture into the Dons half while MK Dons could have added a third through Gerba but Kuipers was equal to his shot.