Captain Conor Hourihane snatched all three points with a stunning volley late on at Nottingham Forest.
The hard-fought encounter looked destined for a goalless draw before the Irishman slammed home a volley from 30 yards out with just two minutes left.
Moments before Hourihane’s dramatic last-gasp winner, substitute Nicklas Bendtner had the ball in the back of the net for Forest, only to be adjudged offside.
Head coach Paul Heckingbottom made three changes to the side that drew against Birmingham City on New Year’s Eve.
One was enforced with Adam Jackson coming in for the suspended Marc Roberts, whilst Adam Hammill and Ryan Williams came in for Sam Morsy and Sam Winnall respectively.
George Moncur returned to the bench after being recalled from his loan spell at Peterborough United.
With all the speculation surrounding whether Wigan Athletic will recall central midfielder Morsy from Oakwell, and whether or not the Reds will trigger the pre-agreed transfer fee if they did, he was left out of the matchday squad.
The Reds had the better of the chances in the first half, but they failed to unlock the door before the break.
The returning Hammill had the first real chance to influence the game as he forced Stephen Henderson into an acrobatic stop to keep out his free-kick early on.
Hammill then teed up Scowen from the resultant corner, with the central midfielder hitting over on the stretch.
Lone striker Tom Bradshaw saw his glancing header well held before Britt Assombalonga hit his own header wide.
Henderson then pulled off two remarkable saves to deny a rampant Scowen a fourth goal of the season from back-to-back corners.
Forest started the second half strongly with Eric Lichaj heading Ben Osborn’s cross over.
A minute later former Middlesbrough man Jackson had to be alert with a sliding challenge to deny Thomas Lam a tap in at the back post.
In the 56th minute the hosts came closest to breaking the deadlock with Jack Hobbs rising highest to meet Osborn’s corner, with his header leaving the crossbar rattling.
The Reds’ defence were caught napping for the first time of the match with seven minutes left as Lichaj was allowed space to turn inside the box but they were let off with his effort ballooning over the bar.
Substitute Bendtner was on the pitch less than two minutes before he sent the hordes of Forest fans into hysterics, only to see the flag up after he put the ball in the back of the net in the 87th minute.
And it was the visitors who had the last laugh as Hourihane chested down and volleyed home from 30 yards out to spark scenes of jubilation amongst Barnsley’s travelling faithful.
Nottingham Forest: Henderson, Lichaj, Mancienne, Hobbs, Cash, Osborn, Dumitru (Vellios, 70), Pereira, Vaughan, Lam (Kasami, 60), Assombalonga (Bendtner, 85).Unused subs: Smith, Grant, Ahmedhodzic, Perquis.
Barnsley: Davies, Bree, Jackson, MacDonald, Yiadom, Hammill, Scowen, Hourihane, Kent (Watkins, 45), Williams (Armstrong, 81), Bradshaw (Winnall, 62). Unused subs: Townsend, White, Evans, Moncur.
Referee: James Linington
Attendance: 22,105 (1,832)