Patrick Bamford and Ryan Lowe sealed a top-10 finish in League One for MK Dons as Stevenage lost for the fifth time in eight matches.
Chelsea loanee Bamford headed in Shaun Williams's cross from close range.
Lowe then rounded keeper Chris Day after dispossessing Mark Roberts 10 minutes after coming off the bench.
James Dunne and Roberts had chances to score but Ian McLoughlin was equal to them as Stevenage failed to find the net for a fifth successive match.
VIEWS FROM THE DRESSING ROOM
Stevenage manager Graham Westley told BBC Three Counties Radio:
"Let's face facts I've had five games here and what I've watched is pretty much what I've seen today - a side that isn't fit enough, that lacks a lot of the basics.
"I've bit my tongue and I've tried to be constructive and positive with them. I've not enjoyed coming in day in and day out and working with the attitudes that are there. There's so much that needs to improve.
"There's people that are going to have to change their attitudes. There are some very good players in there that are just not at the level they're capable of.
"The one thing people know about Stevenage is you turn up and you watch them, there's a pride and a passion. If anyone ever gets anything they've had to earn it and don't tell me MK Dons had to earn anything out there today."
MK Dons manager Karl Robinson told BBC Three Counties Radio:
"We took our goals very very well, Patrick and Lowey finished the season off in style and it's only going to set us up for next season.
"The season's not what we wanted it to be, but there are a lot of highs and again today seeing two Under 17's on the pitch is a tremendous way for us to move forward.
"The two of them (Deli Alli and George Rasulo) are going to go right to the top of English football and we've just got to make sure we nurture them in the right way and enjoy the fruits of their labour, they're very special players.
"We want to build on this year - we've shown when we have all our strong players out, we're a very competitive team and we want them (Stephen Gleeson and Sean Williams) to stay."
Georgio Rasulo takes a shot. Save made by Chris Day. Short corner taken by Shaun Williams from the right by-line.
Shaun Williams has an effort at goal from just outside the area which goes wide of the left-hand post.
Unfair challenge on Max Ehmer by Ryan Lowe results in a free kick. Direct free kick taken by Chris Day.
Unfair challenge on Joe N'Guissan by Mathias Doumbe results in a free kick. Luke Freeman takes the free kick.
Effort from the edge of the penalty area by Joe N'Guissan goes wide of the left-hand post.
Jon Otsemobor has an effort at goal and missed to the left of the target.
Corner taken by Shaun Williams played to the near post, clearance made by Greg Tansey.
Foul by Darren Potter on Marcus Haber, free kick awarded. James Dunne restarts play with the free kick.
Substitution Georgio Rasulo on for Stephen Gleeson.
76:50 Goal scored
Goal! - Ryan Lowe - Stevenage 0 - 2 MK Dons Ryan Lowe finds the back of the net with a goal from inside the six-yard box to the bottom left corner of the goal. Stevenage 0-2 Milton Keynes Dons.
Shot by Shaun Williams from outside the area goes high over the crossbar.
Centre by Dean Bowditch, clearance made by Mark Roberts.
Shaun Williams takes the inswinging corner, Antony Kay takes a shot. Save by Chris Day.
Corner taken left-footed by Shaun Williams from the right by-line to the near post, Header from close in by Darren Potter misses to the right of the goal.
Substitution Patrick Bamford leaves the field to be replaced by Dele Alli.
Free kick awarded for a foul by Gavin Mahon on Patrick Bamford. Stephen Gleeson takes the free kick.
Substitution Greg Tansey on for Matthew Ball.
Booking Antony Kay is shown a yellow card.
Antony Kay gives away a free kick for an unfair challenge on Marcus Haber. James Dunne restarts play with the free kick.
Mathias Doumbe restarts play with the free kick.
Substitution Luke Chadwick leaves the field to be replaced by Ryan Lowe.
The assistant referee signals for offside against Joe N'Guissan.
Free kick awarded for a foul by Darren Potter on Gavin Mahon. Direct free kick taken by Gavin Mahon.
Free kick awarded for a foul by Matthew Ball on Stephen Gleeson. Shaun Williams takes the direct free kick.
Shot by Matthew Ball from deep inside the penalty area misses to the right of the goal.
The ball is delivered by Joe N'Guissan, Luke Freeman produces a left-footed shot from the edge of the area and misses to the left of the goal.
Stephen Gleeson takes a shot. Save by Chris Day. Shaun Williams decides to take a short corner.
Outswinging corner taken right-footed by James Dunne from the left by-line to the near post, Stephen Gleeson makes a clearance.
Darren Potter takes the direct free kick.
Substitution Joe N'Guissan joins the action as a substitute, replacing Lucas Akins.
Free kick awarded for an unfair challenge on Daniel Powell by Max Ehmer.
Foul by Jon Otsemobor on Marcus Haber, free kick awarded. Mark Roberts takes the direct free kick.
Effort from the edge of the box by Luke Chadwick goes wide of the right-hand upright. Corner taken left-footed by Shaun Williams from the right by-line, clearance by Lucas Akins.
Outswinging corner taken by Luke Freeman from the left by-line played to the near post.
The free kick is delivered left-footed by Luke Freeman from right wing, Jon Otsemobor makes a clearance.
Booking Stephen Gleeson receives a yellow card for unsporting behaviour.
Unfair challenge on Marcus Haber by Antony Kay results in a free kick.
Free kick awarded for a foul by Darren Potter on Darius Charles. James Dunne takes the free kick.
The referee blows his whistle to start the second half.
45:00 +1:03 Half time
Half Time The first half comes to an end.
Free kick awarded for an unfair challenge on Lucas Akins by Mathias Doumbe. Free kick taken by Chris Day.
Luke Freeman sends in a cross.
Patrick Bamford is ruled offside. Direct free kick taken by Chris Day.
Luke Freeman fouled by Stephen Gleeson, the ref awards a free kick. The ball is delivered by James Dunne, Mark Roberts takes a shot. Save by Ian McLoughlin. Shot by Mark Roberts from deep inside the penalty area misses to the left of the target.
Gavin Mahon concedes a free kick for a foul on Dean Bowditch. Free kick crossed by Patrick Bamford.
Free kick awarded for a foul by James Dunne on Darren Potter. Stephen Gleeson takes the free kick.
Luke Freeman takes a shot. Darren Potter gets a block in. Corner taken left-footed by Luke Freeman, Headed effort from close range by Lucas Akins goes wide left of the goal.
James Dunne is adjudged to have handled the ball. Free kick taken by Ian McLoughlin.
Matthew Ball takes a shot. Save by Ian McLoughlin.
Unfair challenge on Daniel Powell by James Dunne results in a free kick. Direct effort from the free kick comes in from Darren Potter.
Shaun Williams provided the assist for the goal.
32:58 Goal scored
Goal! - Patrick Bamford - Stevenage 0 - 1 MK Dons Patrick Bamford finds the net with a headed goal from close in. Stevenage 0-1 Milton Keynes Dons.
Shaun Williams delivers the ball,
Dean Bowditch takes a shot. Save by Chris Day.
Marcus Haber sends in a cross.
Mark Roberts concedes a free kick for a foul on Luke Chadwick. Stephen Gleeson takes the direct free kick.
Luke Chadwick produces a right-footed shot from just outside the area that goes harmlessly over the bar.
Darren Potter gives away a free kick for an unfair challenge on Gavin Mahon. Gavin Mahon takes the free kick.
Unfair challenge on Stephen Gleeson by Luke Freeman results in a free kick. Stephen Gleeson takes the free kick.
Dean Bowditch delivers the ball, clearance made by Darius Charles.
The ball is delivered by Shaun Williams.
Centre by Jon Otsemobor, clearance by Darius Charles.
Dean Bowditch produces a cross.
A cross is delivered by James Dunne.
The ball is swung over by Shaun Williams, clearance by Mark Roberts.
Daniel Powell sends in a cross, clearance by Mark Roberts.
James Dunne crosses the ball, Max Ehmer produces a left-footed shot from deep inside the penalty area which goes wide of the left-hand post.
The ball is sent over by Luke Freeman, Mathias Doumbe gets a block in. James Dunne takes a short corner.
Marcus Haber is ruled offside. Direct free kick taken by Ian McLoughlin.
Matthew Ball takes a shot. Ian McLoughlin makes a save.
Substitution Bondz N'Gala goes off and Max Ehmer comes on.
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