United have now gone ten home games without a win but have only themselves to blame for not starting the new year on a victory note.
They dominated the opening 45 minutes, with midfielder Ian Morris twice forcing good saves from Tykes keeper Heinz Muller.
Midfielder Jack Cork and leading marksman Martin Paterson also wasted chances as Barnsley struggled to make an impression.
It was Irishman Morris who finally broke the deadlock firing Scunthorpe in front from close range on the stroke of half-time.
When on-loan full-back Kelly Youga then made it 2-0 when he squeezed an angled shot past Muller in the 47th minute, it all looked over for the visitors.
Visiting skipper Brian Howard missed a chance to get them back into the game when he blazed over from the edge of the box.
It was substitute Grant McCann who reduced the arrears in the 74th minute with a cracking 20-yard volley after his own free-kick had come back off the defensive wall.
The visitors then threw everything forward and Jamal Campbell-Ryce went close with a brilliant 25-yard effort that was tipped over at full stretch by goalkeeper Joe Murphy.
Scunthorpe looked to have held out for what would have been a vital win until the sixth minute of stoppage time when skipper Andy Crosby was adjudged to have handled in the box as he tried to clear a long throw.
Howard stepped up to make no mistake from the spot with his 10th goal of the season.
Scunthorpe now face a difficult second half of the season trying to survive at Championship level and much will depend on how manager Nigel Adkins can strengthen his squad in the transfer window.