While Bradford City were enhancing the division's reputation with a remarkable 4-2 win at Chelsea in the FA Cup, the Dons were busy working on their chances of winning promotion to the Championship come the end of the season.
After a quiet first half, struggling Barnsley looked to have taken control early in the second, but fell behind when Jean-Yves M'voto's attempted clearance fell to a grateful Dele Alli in the 57th minute.
Will Grigg doubled the advantage six minutes later to leave Barnsley two points clear of the relegation zone.
Barnsley's situation looks increasingly perilous after a number of teams below them picked up points.
Colchester United scored one in each half on their way to a 2-0 home win against Leyton Orient, although the hosts did have Elliott Hewitt sent off in the closing stages, while Crewe Alexandra registered a 1-0 win at Port Vale.
Yeovil Town avoided defeat in a goalless draw at home to Coventry City, but there was no respite for basement club Crawley Town - 1-0 losers at Fleetwood Town, who climb above Bradford into the play-off positions.
Peterborough United will be breathing a sigh of relief after bringing an end to their five-match winless run.
Two weeks after chairman Darragh MacAnthony launched a remarkable tirade against some of his players on Twitter, Peterborough picked up a 2-1 win at Notts County.
Marcus Maddison benefited from a deflection as he fired the visitors in front after 13 minutes, before debutant Balint Bajner - whose signing prompted County to block residents of Hungary on Facebook after the club was besieged by comments as part of an internet meme - provided the cross for Garry Thompson to restore parity.
Christian Burgess, though, sealed all three points just after the hour mark.
In the day's other fixture, Gillingham picked up a 3-2 win against Oldham Athletic.
