Karl Robinson's side fell behind in first-half stoppage time courtesy of James Tarkowski's strike before Clayton Donaldson doubled the Bees' advantage with a composed close-range finish.
However, an 80th penalty from Stephen Gleeson and a last-minute header from Izale McLeod ensured the Dons would come away from their penultimate home game with a point.
Having lost Dele Alli and Sanmi Odelusi to injuries at Port Vale, Dons boss Robinson was forced into making two changes to his already thin side, one of which was 17-year-old Giorgio Rasulo, who came in to make his first career League start.
Brentford, having already won promotion to the Sky Bet Championship, had the game’s first chance in the 3rd minute through Adam Forshaw, who produced a smart save out of David Martin with a low 25-yard curler.
Rasulo then had the opportunity to open his Dons account on his first Dons start when David Button’s clearance fell straight to him but, after driving towards the edge of the box, the 17-year-old saw his shot blocked by Tony Craig.
Both teams enjoyed spells of possession in the ten minutes that followed but neither side, bar Brentford from a Douglas header which wouldn’t have counted anyway due to an offside, really threatened to break the deadlock.
In the 22nd minute, McLeod drove to the by-line and cut back for Powell who fired wide of the near post with a first-time shot, before Martin did well to race off his line and prevent Will Grigg from shooting after the Bees striker had beaten the offside trap.
Although there were no clear goal-scoring opportunities in the first half an hour, McLeod did have a decent penalty appeal waved away by referee Tim Robinson - the Dons striker appeared to be tripped by Brentford’s James Tarkowski after getting goal-side of the towering defender but Mr Robinson was unmoved despite strong protests.
Brentford then had the ball in the net in the 35th minute but the linesman on the near touchline deemed Clayton Donaldson to be offside when he tapped home from close-range following a Martin parry.
The Dons came into the game with seven first-team players out injured and an eighth was added to that total just before half-time when Powell was forced off and replaced by Ryan Hall.
And things got even worse for the Dons in the second minute of added on time when Martin failed to hold onto Alan Judge’s corner and Tarkowski found himself in the right place at the right time to prod home an opening goal for the hosts.
Eager not to lose a sixth straight home game, Robinson’s men went in search of an early equaliser after the re-start and Hall shot wide with their first chance, a 25-yard free-kick in the centre of the goal.
McLeod then had a second penalty appeal turned down by Robinson before Lewington went close to latching onto Gleeson’s teasing cross.
In the 56th minute, Judge went close to finding the top left-hand corner with a free-kick but the midfielder, on loan from Blackburn Rovers, put a little too much on it and it flew over.
Then, with a little under an hour on the clock, Brentford doubled their advantage through their leading goalscorer Donaldson, who latched onto Forshaw’s through-ball and finished confidently past Martin from close-range.
In response, Robinson brought on James Loveridge in place of Rasulo but they almost fell even further behind just four minutes later when Dallas broke free inside the box but his left-footed shot hit the side netting.
The men from MK1 hadn’t found the back of the net at stadiummk in seven previous attempts but in the 80th minute the home faithful were finally able to celebrate when McLeod was fouled in the box by Button and Stephen Gleeson fired his spot-kick under the Bees ‘keeper.
The goal set up an interesting final 10 minutes, as the Dons looked to cap off their penultimate home game with a dramatic late finish.
Randall sent a long-range effort agonisingly high of the crossbar in the 82nd minute before Loveridge produced a smart near-post save out of Button with a drilled effort.
Then, with less 60 seconds left on the clock, winger Hall picked out McLeod with an inch-perfect cross and the Dons forward headed home his 10th goal of the season to earn the Dons a share of the spoils.
MK Dons (4-2-3-1): Martin; Baldock, Spence, Lewington (c), Galloway; Smith (Randall 73), Gleeson; Kennedy, Rasulo (Loveridge 67), Powell (Hall 45); McLeod.
Subs not used: Burns (GK)
Goal: Gleeson (pen) 80, McLeod 90
Brentford (4-3-3): Button; Yennaris, Tarkowski (O’Connor 65), Craig (c), Bidwell; Judge (Saville 66), Douglas (Diagouraga 77), Forshaw; Dallas, Grigg, Donaldson.
Subs not used: Lee (GK), Reeves, Trotta, Adams.
Goal: Tarkowski 45, Donaldson 59
Booked: Button, Yennaris
Referee: T Robinson (West Sussex)
Attendance: 10,549 (3,368 away)
Gulliver’s Land Half-Time Jackpot Draw numbers: 11-14-07-03