Looking for points on the road, Town fell behind relatively early on when Ryan Harley broke the deadlock.
At the other end, Francois Zoko had two good chances to level it up either side of the break before Chuks put the result beyond doubt late on.
Needing a turn around in fortunes Darren Way drastically altered his starting eleven with six changes in Buckinghamshire.
In a much-changed back four, Gary Warren returned from a hamstring injury to captain the side alongside the recalled pair of Bevis Mugabi and Carl Dickinson.
Further forward, Matt Worthington and Jake Gray were in favour in midfield as 18-year-old Academy graduate Gabby Rogers stole the headlines by being awarded a first professional start on the right wing.
Courtney Duffus, Omar Sowunmi and Alex Pattison all dropped out with injuries picked up last time out, to see Alefe Santos and Craig Alcock as the only fit players to be excluded.
Much-changed at Stadium MK, the green and whites had some early defending to do in the opening exchanges but looked to have ridden the early storm as Nathan Baxter remained untested between the sticks.
Enjoying some territory at the other end, Warren and Zoko both had headers claimed by Lee Nicholls as the visitors began to tick.
However, not willing to surrender their dominance the Dons took the lead with their first meaningful attempt on goal.
A wide free-kick was only cleared to just outside the box where Harley was on hand to drive a low shot into the bottom corner.
Boosted by the opener, Paul Tisdale’s side enjoyed a monopoly on possession as the game ticked past the midway point of the half, stroking the ball around confidently to the frustration of Town.
Deploying a slow tempo that did little to threaten Baxter’s goal further the game produced nothing of note until 10 minutes before the break.
Enjoying a flurry of territory, Rogers had a dangerous looking shot blocked soon after it left his right-foot before the winger was almost on the end of Gray’s dangerous-looking low cross but for a Joe Walsh clearance.
Restricted to only moments of promise, the green and whites had their best chance of the half on 42 minutes when Zoko picked up the ball 25 yards from goal.
Breezing past Russell Martin to drive into the box, the Ivorian saw his driven effort claimed by a diving Nicholls to round off the half’s action.
With the striker’s shot one of only a few for both sides in the opening 45 minutes, the game’s tempo was raised after the restart with a flurry of early chances.
Conor McGrandles and Kieran Agard were both denied clear strikes on goal by brilliant last-ditch challenges from Dickinson and Waren respectively, before a spell of pressure at the other end.
Beginning to look dangerous in the final third the feeling that a chance was coming continued to grow until a guilt-edged one arrived on 58 minutes.
Alex Dobre dribbled his way into a crossing position where he picked out Zoko perfectly in the middle, but the striker’s first-time shot was curled just wide from no more than 10 yards out.
Roared on by the travelling faithful behind the goal a succession of corners followed, but an equaliser wasn’t to come as Ryan Seager and Alex Fisher were introduced.
Not interrupting the visitors’ dominant spell the freshly introduced Seager dragged a shot wide from the edge of the box, as Town continued to battle for an equaliser at Stadium MK.
Sensing their lead was in danger, the Dons looked to avoid a nervy final 10 minutes and managed to do so thanks to some solo brilliance.
Introduced at the break, Aneke picked the ball up on the touchline and drove inside to ghost past a host of challenges before firing home from close range to deliver a major blow on 82 minutes.
Deserving more for their second half display, the green and whites battled until the end but couldn’t find a goal for their efforts as Way’s side suffered defeat once again.
MK Dons: Nicholls; Martin, Houghton, Walsh; Brittain (Cisse 71′), Gilbey (McGrandles 15′), Harley, Lewington; Agard, Hesketh, Wheeler (Aneke 46′).
Bookings: Wheeler 38′, Hesketh 43′
Subs not used: Moore, Simpson, D’Ath, Watson.
Yeovil Town: Baxter; Grant, Warren, Mugabi, Dickinson (Ojo 68′); James (Seager 61′), Worthington, Gray; Rogers, Zoko (Fisher 61′), Dobre.
Subs not used: Nelson, Gafaiti, Arquin, Abrahams.