Boos reverberated around Oakwell at the final whistle after Murray Wallace's 89th-minute header condemned the Reds to a third consecutive defeat, a result which leaves the South Yorkshire club 22nd in the Championship.
And it wasn't just the latest in a long sequence of disappointing results that will have left the home faithful displeased, their team having been comfortably second best for all but the opening 20 minutes of the contest.
The Reds began brightly, with the lively Aaron Leya Iseka taking aim from outside the Millwall box and forcing Bartosz Bialkowski to get down low and tip his second-minute strike around the post.
Cauley Woodrow then drilled the ball across the face of goal and saw the ball deflected behind for a corner, from which Michal Helik stabbed an instinctive effort narrowly wide.
At the other end, George Evans wasn't too far away from breaking the deadlock with a curling effort that had Brad Collins clawing thin air on its way past the home custodian's left-hand post.
A glorious chance for Barnsley to take the lead then came, and went, on 18 minutes as Devante Cole was played clean through, but failed to beat the advancing Bialkowski.
Having failed to capitalise, the Reds visibly dropped off off from the midway point of the opening period and Millwall finished the half looking much the more likely.
Collins had to touch Murray Wallace's goal-bound blast over his cross-bar in the 20th minute, while a stretching Benik Afobe was centimeters away from getting on the end of a dangerous left-wing cross at the far post.
The second 45 unfolded in similar fashion, with Barnsley looking devoid of ideas going forwards, while the visitors continued to engineer some promising opportunities.
Only a perfectly-timed last-ditch sliding challenge by Liam Kitching thwarted Jed Wallace as he raced clear on 50 minutes and shaped to slide the ball beyond an exposed Collins.
A succession of timely blocks in and around their own six-yard box then saw the hosts survive a goalmouth scramble before Collins did well to deny former Reds striker Tom Bradshaw one-on-one with a near-post block.
It took Barnsley until the 85th minute to fashion their only decent sight of goal of the half and when it arrived, Callum Brittain sliced a poor effort wide of the near post when he ought to have done much better.
With Millwall very much in the ascendancy and the Reds looking rather devoid of belief or ideas, a late goal for the away side seemed almost inevitable, and duly materialised on 89 minutes.
Jed Wallace delivered a corner from the left and Murray Wallace timed his arrival at the back post to perfection, directing a powerful downward header into the back of the home net from just a couple of yards out.
Barnsley finally showed something resembling intent and urgency during stoppage-time, though this amounted to little more than a couple of hopeful crosses into the Millwall box, and the Lions saw the game out with ease.