Both sides hit the woodwork before the break – on-loan Chelsea teen Lewis Baker for the visitors, Gareth Evans for the hosts.
But the game came alive in the second half – Fleetwood squandering a golden opportunity to pull ahead before a sucker punch from Karl Robinson’s men.
Fleetwood, comfortable to counter in the opening 45 minutes, had taken the game to the Dons, whose keeper David Martin almost suffered a calamity when he spilled Conor McLaughlin’s teasing curled cross – David Ball unable to pounce before he snapped it back into his arms.
Antoni Sarcevic then produced a determined run to the dead ball line, Evans unable to convert after a superb delivery to the penalty spot.
And from the break Dons scored, Rob Hall’s cross flicked on by Spurs man Alli and Baker tapping home.
The hosts kept battling but were sunk by a double salvo – MK adding two in three minutes to put the game beyond reach.
First Will Grigg left Stephen Jordan standing and slotted low past Maxwell to double the advantage.
Then, Alli popped up in the box to apply a stunning right footed half-volley to Dean Lewington’s cross, a stunning finish to announce the Dons’ intentions to push Preston, who squandered a two-goal lead to draw with Gillingham, all the way for second spot.