The first period was a tight affair but United had the better second half but just could not find the back of the net after Jean Yves-M’Voto was sent off with more than half an hour remaining and increased pressure from the Claret and Blue.
Mark Robins made just one change for the visit of his former club as he looked to make it three home wins on the bounce after seeing off Chesterfield and Swindon.
George Evans made way for Isaiah Osbourne to start, while Alex Davey remained absent from the matchday squad through injury. Former Iron Sam Winnall was not in Barnsley’s matchday squad on what would have been his first return to the club.
The Iron had a couple of early chances in the game. The first came as Paddy Madden found space to get a shot off on the right side of the area and he shot straight at goalkeeper Adam Davies.
The Tykes’ Conor Hourihane went close with a good low free-kick from 20 yards - it went across goal and hit the outside of the post.
A defensive mix up saw Hourihane capitalise and persist and his shot was well saved by Daniels, still sporting a black eye from Saturday’s game at Preston.
United grew into the game as a quick break saw Madden smash the ball against the side netting and then Davies was tested as Boyce, van Veen and O’Neil had shots before the break.
Boyce and Canavan combined well to clear after pressure from the lively Hourihane, who then hit the target with a 25-yard drive, but Daniels gathered it well.
Jordan Clarke was alert to make an excellent block after good work from John O’Sullivan which saw Josh Scowen shoot.
Neal Bishop was cautioned after coming together with James Bailey and he will now serve a two-match suspension after accumulating ten yellows this term.
Marcus Williams picked up an injury before the break and, while he was clearly eager to carry on, he had to be substituted, with Eddie Nolan coming on in his place.
Kevin van Veen had the first chance of the second period, when he latched onto a ball on the left and Davies saved it brilliantly with his feet.
Barnsley opened the scoring on 51 minutes when Scowen latched onto a defensive error and he finished wonderfully from a tight angle to send the visiting fans into hysterics.
It was nearly two just moments later, after Reds captain Martin Crainie curled an effort over and the visitors were reduced to ten men when Yves-M’Voto made a rash challenge on Tom Hopper and received his second booking.
The Iron, clearly boosted by the red card, soon went close as Bishop had a bouncing shot tipped over the bar by Barnsley’s goalkeeper.
Madden had a goal disallowed on 64 minutes, when he latched onto Nolan’s lob and finished well, just moments before Hopper nearly found an opening but he was also adjudged to have made an early run.
Barnsley rarely created chances as Bailey sent a long-range effort over from distance and Scowen fizzed a curling effort across goal but that was all as United searched for an equaliser.
A great delivery from McSheffrey saw Boyce’s powerful header tipped over fantastically by Barnsley’s Davies.
Robins tried to alter things as he brought on George Evans 17 minutes from time but Daniels was the next to be called upon after scrambling at Hourihane’s feet following a dangerous run down Barnsley’s right-hand side.
Davies dropped his first ball of the night and United could not react quick enough to convert. Despite five minutes of added time and a glancing header from Madden, the managerless Tykes left North Lincolnshire with the full three points.
Scunthorpe United: Daniels, Clarke, Boyce, Canavan, Williams (Nolan, 42), Bishop, O'Neil (Evans, 73), Osbourne (McSheffrey, 64), Madden, Hopper, van Veen.
Substitutes not used: Anyon, Adelakun, Wootton, Llera.
Barnsley: Davies, Cranie, Nyatanga, M'Voto, Smith, O'Sullivan (Holgate, 58), Hourihane (Berry, 90+2), Pearson, Scowen, Bailey, Waring (Oates, 90+2).
Substitutes not used: Dibble, Lita, Hemmings, Lalkovic.
Attendance: 3,508 (595 away).