Steve Claridge had cancelled out Ben Harding's 58th minute opener for the Dons, but stand-in skipper Lewington smashed in his first goal of the season from 25 yards to grab three vital points for Danny Wilson's boys with almost the last kick of the game.
The win was all the more remarkable as the Dons played the whole second half with striker Aaron Wilbraham in goal due to injuries to Ricardo Batista and Matt Baker on the day.
Dons' manager Danny Wilson made two changes to the team that lost 5-0 at Huddersfield last Saturday, with Filipe Morais back from Portugal Under 21 duty and Trent McClenahan recalled to the starting line-up.
Baker was dramatically plucked from the stand 10 minutes before kick-off to continue in goal after Batista, also back from Portugal international duty, injured his finger in the warm-up.
Skipper Paul Mitchell was dropped for the first time this season, while Ben Chorley missed out with an Achilles injury.
Bradford boss Colin Todd made two changes to the team that drew 1-1 with Bristol City last Saturday, with Owen Morrison replacing Lewis Emanuel and Claridge coming in for the suspended Dean Windass.
Steven Schumacher returned from suspension in place of Bobby Petta, who was serving his own ban.
Milton Keynes started brightly and Bantams' defender Mark Bower was forced to clear Morais' dangerous low cross from under his own crossbar inside the first minute with Wade Small lurking behind.
At the other end, Marc Bridge-Wilkinson fired a 25-yard free-kick inches wide for Bradford in the fifth minute.
But the Dons continued to dominate and Damian Stewart's terrific last-ditch tackle prevented Scott Taylor opening the scoring for the hosts two minutes later.
And then Bantams' skipper David Wetherall produced a fantastic lunging block to deflect Gareth Edds' goal-bound shot over the bar after Taylor's cut-back had found him unmarked 12 yards out.
Schumacher wasted Bradford's best chance of the first half in the 39th minute when he latched onto Tom Penford's through ball but dragged his shot wide from edge of box.
McLeod lobbed a good chance well over the bar for the Dons four minutes before the break, before Bower had a goal ruled out for the Bantams on the stroke of half-time.
Bower's header from Bridge-Wilkinson's corner flew into the net but the effort was chalked off for a foul on Dons' keeper Baker, who was forced off with a knee injury incurred in the incident.
Striker Aaron Wilbraham was forced to replace Baker between the sticks at half-time as Dons' manager Wilson did not have a keeper on the bench.
But Milton Keynes continued to press and after Morais had gone close with two long range strikes, Harding put the Dons ahead in the 58th minute.
Morais' cross-shot was tipped onto the bar by Bantams' goalkeeper Donovan Ricketts and Harding rammed in the rebound from eight yards.
Substitute Clive Platt almost doubled the Dons' advantage four minutes later but Ricketts kept out his close range effort, before Claridge equalised for Bradford in the 65th minute.
Bridge-Wilkinson's corner caused panic in the Dons' box and as the hosts failed to clear their lines, Claridge capitalised on the uncertainty to poach his fifth goal of the season from five yards.
David Partridge should have restored the Dons' lead in the 68th minute but his strike from six yards was deflected wide, before Ricketts produced a magnificent save to tip Edds' 25-yard half-volley out of the top corner in the 76th minute.
But after Harding had gone close with a 22-yard strike that flew inches wide, skipper Dean Lewington smashed a 25-yard drive injury-time thunderbolt into the top corner to send the home fans wild.