With the leading pair of Brentford and Wolves both out of action - their respective games with Crawley Town and Stevenage being postponed - Russell Slade's side had the opportunity to move to the summit with three points against Peterborough.
All looked to be going to a plan when Dave Mooney broke the deadlock on 70 minutes, but two goals in the final two minutes from Britt Assombalonga and Tommy Rowe turned the game around and handed Darren Ferguson's men a third League One win in four.
Fourth-placed Preston North End kept up their play-off challenge with a 2-1 win at Tranmere Rovers thanks to two goals from Joe Garner, who scored either side of Ash Taylor's equaliser.
Rotherham United, in fifth, were not in action after their fixture at Colchester United was called off due to a waterlogged pitch, while seventh-placed Walsall missed out on the chance to climb into the top six when they were well beaten 3-0 at home by Milton Keynes Dons.
Izale McLeod put the visitors in front on the half-hour mark, before things went from bad to worse for the hosts as Andy Butler was dismissed for a foul on McLeod inside the area, and Ben Reeves tucked away the resulting penalty.
McLeod added a third with 20 minutes remaining before Walsall's Michael Ngoo missed from the spot to complete a miserable day for the home side.
At the wrong end of the table, Sheffield United built on their midweek FA cup success at Fulham by claiming a crucial 2-0 home win over fellow strugglers Shrewsbury Town.
Goals in the first 17 minutes from Ryan Flynn and Stefan Scougall earned Nigel Clough's side their first league win in five matches and moved them to within a point of safety.
A place above them and just outside the relegation zone are Carlisle United, who lost 2-1 at home to Gillingham, while Bristol City earned a point with a 1-1 draw at Oldham Athletic.
Elsewhere, Notts County pulled off a surprise result by seeing off high-scoring Coventry City 3-0 at home, while Swindon Town came from two down to win 3-2 at Port Vale and Bradford City and Crewe Alexandra played out an entertaining 3-3 draw.
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