Goals at the start and finish of the game bookended a miserable afternoon for Rovers as they succumbed to a third successive defeat.
The home side got off to a terrible start as Quansah upended Leko in the box in the second minute, giving referee Boyeson no option but to award the spot-kick. Eisa fired home down the middle of Mem debutant Balcombe's goal.
Balcombe was soon back in the action, pulling off a stunning diving stop in the 11th minute, clawing Eisa's shot away.
Coutts was booked in the 17th for preventing an MK counter-attack.
The biggest cheer of the afternoon thus far came in the 20th minute when the perpetually-fouled Coburn was awarded a free-kick. The set-piece found its way to Collins and his header looked like it was going to loop in for the equaliser, but drifrted agonisingly wide.
Rovers were enjoying the lion's share of possession but a packed MK defence was dealing comfortably with the pressure. A misplaced Balcombe pass in the 32nd minute handed the visitors a corner, but thankfully the Gas cleared their lines.
The referee spoke to Connolly and Eisa after a coming together, but took no action against either. Meanwhile, Collins and Sinclair switched flanks to see if it would bring about a change in fortunes.
Devoy was booked in first-half injury time for a late tackle on Ward.
Rovers began the second-half without skipper Paul Coutts, as he was replaced by Ryan Loft. The big striker was almost on the scoresheet in the 50th minute, glancing just wide from a Collins cross.
Finley saw yellow as tempers became frayed in the 58th minute. Five minutes later, McCormick replaced Sinclair.
Gibbons did well to block a Devoy shot to give Dons a corner in the 66th minute. Moments later, the Gas right-back was scythed down by an awful tackle from Maghoma, who was lucky to escape with just a yellow card.
Leko was next in Boyeson's book in the 75th minute, followed a minute later by Johnson as MK resorted to some crude tackles.
Grant Ward was now playing deep, looking to dictate play on an impressive home debut for the Gas. Marquis and Anderson entered proceedings.
Quansah denied Eisa a certain goal in the 83rd minute with a last-ditch tackle and James Connolly blocked a goaldbound shot from the resulting corner. Aston Villa youngster Lamare Bogarde replaced Ward in the 85th minute. His first touch was a deft pass to Collins, his second a lovely reverse pass to Marquis.
With Rovers pushing forward and looking for the equaliser, the visitors caught them on the break, with Eisa playing in substitute Dean to make it two-nil.
Bogarde was inches away from a consolation, curling narrowly wide from outside the area.
Next up for Rovers is a Sky Bet League One game at Lincoln City on Saturday 11th February.
Rovers: Ellery Balcombe, James Connolly, Lewis Gordon, Jarell Quansah, Sam Finley, Grant Ward, Aaron Collins, Paul Coutts (c), James Gibbons, Josh Coburn.
Subs: Anssi Jaakkola, John Marquis, Ryan Loft, Harry Anderson, Lamare Bogarde, Luca Hoole, Luke McCormick.
MK Dons: Jamie Cumming, Tennai Watson, Jack Tucker, Josh McEachran (c), Mo Eisa, Jonathan Leko, Daniel Harvie, Sullay Kaikai, Dawson Devoy, Zak Jules, Paris Maghoma.
Subs: Franco Ravizzoli, Will Grigg, Bradley Johnson, Conor Grant, Darragh Burns, Henry Lawrence, Max Dean.
Referee: C Boyeson
Attendance: 8,429