Andy Ritchie's promotion-chasers had two goals ruled out and hit the woodwork twice through Barry Conlon and substitute Mark Richards in the 90th minute.
Tykes boss Andy Ritchie made one change to the team that won 3-0 at Gillingham in midweek, with Robbie Williams coming in for Dale Tonge.
Tonge dropped to the bench, where he was joined by Bobby Hassell after his recovery from a knee injury.
Dons manager Danny Wilson re-shuffled his pack after the 3-1 home reverse to Swansea, bringing Gary Smith and Nicky Rizzo into the midfield at the expense of Nick McKoy and Leon Crooks.
MK Dons were quick out of the blocks and skipper Paul Mitchell was the first to threaten, blasting just wide on the volley after the ball fell kindly for him on the edge of the box in the first minute.
Barnsley settled into their stride and a good flowing move culminated in Paul Hayes being denied by goalkeeper Matt Baker in the 10th minute.
Just moments later the Dons should have taken the lead when full-back Williams was caught napping by Rizzo's ball over the top, but the pacy Izale McLeod smashed his half-volley over the bar from 10 yards.
And as the Dons began to take control, only a last-ditch tackle by Williams prevented McLeod opening the scoring from close range after he latched on to Clive Platt's header, before Smith's 25-yard drive forced Nick Colgan into a save low to his left.
At the other end the Reds thought they'd taken the lead just after the half-hour mark when Conlon headed in Chris Shuker's pin-point cross from close range but the effort was ruled out for offside.
And then the unlucky Conlon came close to breaking the deadlock again on the stroke of half time, but his header from Williams' cross looped on to the top of the bar.
Tykes substitute Daniel Nardiello came on for Hayes in the 63rd minute as the game was drifting towards a stalemate and he immediately sparked them into life.
Williams and Conlon were denied by smart saves from Baker before Nardiello shrugged off Craig Morgan and finished well but he was flagged for fouling the Welshman.
The former Manchester United trainee had another effort saved before he twisted and turned on the edge and fired in a fierce strike that Baker tipped over the bar.
Milton Keynes came back into the game and pressed for a winner without creating any clear-cut openings, but it was Barnsley substitute Richards who almost stole the points with a 90th minute glancing header that hit the bar from Jacob Burns' corner.