Dean Bowditch and Daniel Powell gave MK Dons the first half lead and Ben Reeves extended their lead with only 20 minutes remaining.
Turner then grabbed a goal back for Latics ten minutes from time but that was not enough and Dons grabbed all three points.
Dons could have taken the lead early into the game through striker Will Grigg.
The striker capitalised on an error from goalkeeper Jake Kean but after rounding the goalkeeper, he struck the post and it went behind for goal kick.
Latics grew into the game with Jonathan Forte looking dangerous on the left wing.
He danced through the defence on 15 minutes but his through ball towards Conor Wilkinson was just cut out by Kyle McFadzean.
It was Forte again who threatened a couple of minutes later. He raced to the byline, crossed into the centre but it was just ahead of Connor Brown who was surging into the penalty area.
Kean was forced into a wonder save midway through the half as he denied Grigg from six yards but the goalkeeper excellently turned the ball past the post.
Minutes later, however, MK Dons took the lead, slightly against the run of play.
A lack of communication in defence saw Samir Carruthers profit and he fed Bowditch in space who placed the ball beyond Kean to give Dons the lead.
After the half hour mark, Latics had their best spell of the game and should have drawn level.
Forte was the main instigator and his energy caused the Dons defenders to back track but his one-two with Wilkinson was picked off just as he was about to shoot from inside the area.
Latics had the ascendancy and Winchester played an inch-perfect through ball to the top scorer two minutes later but his shot was well blocked by David Martin.
Dons managed to catch Athletic on the counter attack and doubled their lead on 37 minutes.
Carruthers picked the ball up on the left hand side, drove inside the penalty area and shot. Kean managed to parry the effort but only into the path of Powell who bundled the ball over the line to extend Dons' lead.
Athletic needed a response at half time and brought on Danny Philliskirk in place of Connor Brown and they came out with a lot more energy in the second half.
Philliskirk drove at the defence, fed Jones on the left who headed to Wilkinson in the centre and his shot smacked the upright and away from danger.
Wilkinson again could have pulled a goal back for Latics only a minute later but he shaped his shot just wide of the post from 25 yards.
Latics were forced into their second change of the night as Kean picked up an injury and was replaced by youngster Joel Coleman, who made his senior debut for the club.
The home side continued to press and Mike Jones, who captained the side in the absence of Adam Lockwood and Liam Kelly, whipped a free kick which almost deceived Dons' goalkeeper but he saved well.
Again, after all Latics' hard work trying to get back into the game, they were undone by a wonder strike on 65 minutes.
Coleman was left with no chance as Reeves shaped to shoot from 25 yards and curled the ball into the top corner to make it three.
Dons really should have made it four with only 20 minutes remaining but Grigg failed to trouble Coleman from eight yards.
That was a let off for Latics and with only ten minutes of the game remaining, they did manage to pull a goal back.
Substitute Rhys Turner knocked the ball into his path and finished confidently past the Martin to reduce the arrears.
Latics had a go in the last ten minutes with Turner causing a nuisance of himself in attack.
The 19-year-old and full back Mat Sadler almost combined to pull another goal back for Latics but the ball went just past the post.
As five minutes of additional time was announced, Forte shot from the edge of the box which deflected off Turner but Martin saved well.
Oldham Athletic: Kean (Coleman 57'), B.Wilson, Brown (Philliskirk 46'), Kusunga, Dieng, Sadler, Woodland, Winchester, Jones, Forte, Philliskirk, Wilkinson (Turner 73').
Subs not used: Truelove, Bove, Jacobs.
MK Dons: Martin, Hodson, Lewington, McFadzean, Kay, Bowditch (Baker 52'), Reeves (Randall 90'), Grigg, Powell (Spence 90+3), Carruthers, Baker.
Subs not used: Green, Walsh, Cole, Burns.
Goals: Oldham Athletic (Turner 80') 1-3 MK Dons (Bowditch 25', Powell 37', Reeves 65')
Attendance: 2,455 (66 visiting supporters)