Wanderers’ memorable season ended at the penultimate hurdle as a single goal was enough for Barnsley to deny the Whites a second Wembley trip.
Liam Kitching’s first-half header ultimately separated the sides over two legs of their play-off semi-final.
With Wanderers – superbly backed by the travelling fans – unable to turn a dominant spell after half-time into an equaliser the night ended in heartache.
But once the immediate pain has subsided, Ian Evatt’s men can look back on a campaign of an enormous progress with the Papa Johns Trophy in the cabinet and play-off campaign contested thanks to a top-six finish in just a second season in the division.
Wanderers made two changes to their starting line-up for what had become a winner-takes-all showdown following last Saturday’s drawn first leg.
George Thomason returned in midfield, with Dan Nlundulu getting the nod to start up front alongside Dion Charles, who had an early sight of goal with an effort he struck at Harry Isted after being found by Randell Williams.
James Trafford was the busier of the two keepers in a frantic start, although most of his work was done in keeping out efforts from outside the penalty area – the best of which came from Herbie Kane.
Most of the pressure came from the home side but when they did go ahead after 24 minutes it was in controversial fashion.
Referee Michael Salisbury awarded a free-kick to the Tykes after Nicky Cadden had clearly caught Eoin Toal with Wanderers in possession.
And while the Whites dealt with the initial danger, Barnsley were able to re-cycle the ball for Luca Connell to cross and Kitching to head home.
Wanderers needed to maintain their composure and try and get a foothold in the contest as Barnsley never allowed them a moment to build up any momentum.
A brighter start to the second half hinted at better as Williams had the opportunity to find Charles in the box and Charles then robbed Kitching to give Conor Bradley the chance to burst into the box before running into red shirts.
With the Wanderers’ fans doing everything to lift their side the Whites were enjoying their best spell of the game as they built up the pressure in search of an equaliser.
Twice Thomason had efforts in the box blocked and Barnsley were barely allowed of their half for a time as roles were reversed.
Wanderers needed to make it count, though, and with 25 minutes to go – and moments after Adam Phillips hit the bar for the Tykes – Evatt made a double change to try and find a catalyst as Elias Kachunga and Barnsley old boy Victor Adeboyejo were given the chance to make a difference.
When Adeboyejo almost got in behind the hosts’ defence he forced Mads Andersen into a back-pass Isted handled but from the free-kick touched to him, Aaron Morley lifted his effort inches too high.
The clock was against Evatt’s men as they tried to at least force extra-time and keep their hopes alive.
But they kept trying to force the issue and create the one big chance that could turn the tie with Cameron Jerome the final substitute introduced to provide a further presence up front.
Instead, there were only half-openings but Wanderers kept going to the end and gave everything in a bid to sustain promotion hopes which will now have to be revived next season.
Wanderers: Trafford; Toal, Almeida Santos, Johnston; Bradley, Morley (Jerome 85), Thomason; R Williams (John 73); Dempsey (Sheehan 73); Charles, Nlundulu. Substitutes: Dixon, MJ Williams.
Booked: Dempsey, Santos
Barnsley: Isted; B Thomas, Andersen, Kitching; Connell (Russell 85); Williams, Phillips (Benson 85), Kane, Cadden; Tedic (Norwood 65), Cole (L Thomas 87). Substitutes: Collins, Cotter, Watters.
Booked: Cole
Referee: Michael Salisbury
Attendance: 16,274 (2,181 Wanderers)