Barnsley went in front as early as the fifth minute when on-loan striker Jamie Cureton, coming back from behind the last Burnley defender, received a pass and put a 20-yard right-foot shot beyond Brian Jensen.
Burnley struggled to make an impact early on in the match and their only real opportunity came when a Robbie Blake corner found the head of captain Steven Caldwell but he put his effort wide of the target.
A mistake on 26 minutes by central defender Darren Moore gave Wade Elliott a run on goal but he shot tamely wide.
Six minutes later a free-kick from Blake was pushed away by Heinz Muller diving to his left to make the save.
The home side equalised eight minutes before the interval when Blake outwitted Moore near the touchline and crossed low to the far post for Chris McCann to score.
Burnley could have gone in front within 60 seconds but Chris Eagles was denied by goalkeeper Muller.
However, with three minutes of the first half remaining, Burnley carved out a glorious opportunity when Graham Alexander's delightful pass sent Martin Paterson clear for the striker to set up Eagles on the six-yard box but he somehow missed the target with his effort.
Striker Cureton sent Jamal Campbell-Ryce racing clear of the Burnley defence but Jensen stuck out a leg to make the save.
At the other end Eagles set up Blake but he placed his shot just over the crossbar.
The winning goal came on 67 minutes when Campbell-Ryce's attempted cross took a big deflection off Clarets skipper Steven Caldwell giving goalkeeper Jensen no chance.
Eagles had a couple of opportunities to make amends for his glaring miss but was denied on both occasions by Muller.
Just to show that it was going to be one of those games for the former Manchester United youngster, his game was summed up in the fifth minute of stoppage time when he hoisted a free-kick deep into the midst of the visiting supporters.