The Clarets suffered back-to-back defeats for only the second time this season as an early goal from Romal Palmer was enough to give the Tykes victory.
Palmer headed improving Barnsley to their sixth win of the season and pulled them further clear of bottom club Hull City as Burnley drew a blank in front of goal for the second game in a row.
But whereas they were unfortunate to finish pointless in Monday’s defeat to Sheffield Wednesday by the same scoreline, the Clarets could have no complaints at leaving the Oakwell Training Ground empty-handed.
Victory would have taken Steve Stone’s side back level with Birmingham City and Leeds United at the top of the Professional Development League’s northern group.
But with the likes of Dwight McNeil, Ali Koiki and the injured Olly Younger unavailable this is now a more youthful line-up on a steep learning curve.
Scholars Bobby Thomas and Matty Rain made up two members of the back four as they were given an opportunity to impress.
The powerful Thomas, 17, seized his chance with a commanding display at centre-back, while left-back Rain held his own on his debut.
But in front of them it was hard going trying to piece together any constructive football on a difficult surface where battling qualities came to the fore.
Barnsley showed more of those, as well as moving the ball better, and in a sluggish start the Clarets were punished after 10 minutes with what proved to be the winner.
Jordan Barnett, who was released by the Clarets at the end of last season, had delivered a number of dangerous balls into the Burnley box from his left-back berth.
And when he switched flanks to whip in a free-kick, Tykes captain Palmer flashed home a near-post header.
In a scrappy first half devoid of chances, Palmer was closest to getting on the scoresheet again a minute before the break as Barnsley held sway.
Anders Lindegaard came out to save at the feet of the striker but from almost on the byline Palmer was able to scoop the loose ball against a post.
From there the Clarets broke with Tinashe Chakwana getting free for an effort he dragged across the face of goal.
But that was a rare opening for a Burnley side which struggled to impose itself on a pitch not conducive to tidy passing or running with the ball.
Set-pieces remained arguably the best route to goal and Barnsley twice had opportunities to add to their lead early in the second half.
Firstly, Sam Fielding headed over the top and centre-back partner Jasper Moon was then denied by a fine save from Lindegaard, who smothered with his legs.
Barnsley were then unfortunate not to be awarded a penalty as Barnett appeared to be tripped in the box.
But the Clarets finally began to carry a threat in an improved second-half showing as they pushed for an equaliser late on.
The introduction of Rob Harker added a presence up front and after he volleyed into the side netting, Josh Benson flicked an effort just wide from Jordan Cropper’s low cross.
Marley Blair then shot off target after being pushed wide by Barnett but Stone’s youngsters were never able to create the clear opening they needed to potentially grab a point.
And it was Barnsley who almost struck again to spare any late anxiety when the lively Louis Walsh broke clear and brought another sharp save out of Lindegaard.
Barnsley: Kendrick, Helliwell, Barnett, Fielding, Moon, Otim, Walsh (Binns 90), Ward, Feeney (Willard 85), Palmer, Berkovits. Substitutes: Simpson, Gagen, Ogberbor-Onaiwu.
Burnley: Lindegaard, Cropper, Rain, Benson, Thomas, Glennon, Bayode, Howarth, Chakwana, Agyei (Harker 59), Blair. Substitutes: Stone, Kershaw, Woods, Cook.