Teenage prodigy Reuben Noble-Lazarus scored his first senior goal to deny Lions boss Kenny Jackett victory in his 200th game at the helm as Barnsley edged to victory at Oakwell.
Noble-Lazarus, who made his debut for the Yorkshire club as a 15-year-old, stepped off the bench as a second-half sub and slammed home a 20-yard drive on the hour-mark to secure victory.
It was harsh for Jackett and his team to finish empty-handed, having enjoyed by far the better of possession in the opening half and creating a number of opportunities after the break, including a Tam Mkandawire header that smacked the woodwork deep in injury-time.
On paper this game could easily have had an 'end of season' feel about it, with Barnsley safely positioned in mid-table and The Lions' Play-Off hopes over following last weekend's defeat by Swansea City.
"We were poor with our shooting, our crosses, our final ball and we were very casual going forward and I was disappointed today," said Kenny.
"Overall we finished ninth in the table and that is fantastic for Millwall, but overall I was very frustrated with us going forward. We can do a lot better than that."
Manager Jackett made five changes to his starting line-up and after the opening exchanges in which both teams took a while to get to grips with a slippery playing surface, the game opened up and improved as a spectacle.
Millwall, with Hamer Bouazza and Andros Townsend in particular, teasing and tormenting the Barnsley full-back pairing of Matt Hill and Bobby Hassell looked the most likely source of prising an opening.
And it nearly arrived around the 20-minute mark when an almighty goalmouth scramble ensued from Townsend's dinked delivery with Mkandawire and Darren Ward getting a boot and head to the ball respectively before the danger was averted.
Former Lion Danny Haynes broke quickly down the right flank but then slipped at the most inopportune moment as he prepared to cross with Barnsley's first really incisive attacking move midway through the half.
On 24 minutes Steve Morison picked up the ball from Jimmy Abdou just inside the Barnsley half, but with no real options ahead of him he went it alone and hit a low drive straight at keeper Luke Steele.
Morison was involved again 60 seconds later, providing a neat lay-off for right-back Alan Dunne and his low drive was comfortably held by Steele.
Mkandawire's hooked shot from a Townsend cross had the power but lacked direction and then both Townsend and Josh McQuoid tried their luck from distance to no avail.
Townsend then forced Steele into the save of the half with a 20-yard fizzer that the Barnsley man instinctively stuck out a hand to divert away from the goal as The Lions pressed for an opening goal before the break.
But it was Barnsley, and teenage sub Noble-Lazarus, who made the all important breakthrough on the hour mark with the youngster's crisp drive nestling into the bottom corner despite keeper David Forde appearing to get the slightest of touches to the ball.
On came James Henry and John Marquis for Hamer Bouazza and McQuoid and it was Marquis who was a whisker away from scoring with his very first touch, only for Man of the Match Steele to block his effort before claiming Morison's underhit return shot.
Neil Harris came on for Morison shortly after and it was from his late delivery that Mkandawire sent a powerful header against the post as The Lions tried, and failed, to haul themselves level.
Although the final whistle might have brought the curtain down on the current campaign with a performance sadly not on par with the level Lions fans have come to expect, it has been another 12 months of tremendous progress under Jackett and his backroom team.
This season, Millwall's first back in the Championship after what felt like an eternity in the wilderness, has seen the seeds of the club's recovery grow and take root.
The sheer strength of those roots holds so much hope for the future.
Without doubt, it has been another season of progress, not perfection, for the club. And for every member of the Millwall family, long may that continue.
Barnsley: Steele, Butterfield, Doyle, Foster, Trippier, Hill (McEveley, 65mins), Gray, Haynes (O'Brien, 90+3mins), Shackell, Hassell, Mellis (Noble-Lazarus, 46mins). Subs not used: Preece, Stones, Clark, Rose.
Bookings: Doyle (66mins), Haynes (70mins)
Scorer: Noble-Lazarus (59mins)
Millwall: Forde, Dunne, Craig, Abdou, Robinson, Ward, Bouazza (Henry, 60mins), Mkandawire, Morison (Harris, 72mins), McQuoid (Marquis, 60mins), Townsend. Subs not used: Mildenhall, Hackett, Smith, Purse.
Bookings: Bouazza (52mins, Dunne (65mins), Henry (90+4mins)
Ref: M Russell