Boss Jon Brady issued a defiant message after 10-man Northampton saw automatic promotion back to League One snatched from their grasp.
Instead of an immediate return to the third tier, Town face a play-off semi-final against Mansfield after being pipped to third place by Bristol Rovers on goals scored.
Northampton won 3-1 at Barrow but were still overhauled by Rovers, who hit seven past Scunthorpe.
It looked plain sailing for the Cobblers after 21 minutes as Sam Hoskins scored his 13th and 14th goals of the season and Scott Horsfall headed home to make it 3-0.
But Josh Kay headed a consolation for Barrow after 44 minutes and Rovers ran riot in the second half of their match at the Memorial Stadium to change the complexion of the afternoon completely.
Northampton even had goalkeeper Liam Roberts sent off late on for handling the ball outside his area and he will miss the semi-final first leg.
Still the 10-men almost grabbed a decisive fourth, but Hoskins was denied a hat-trick by Paul Farman’s fine save.
“It is pretty hard to comprehend,” said Brady. “We will dust ourselves down and get ourselves ready for the play-offs.
“They are a hugely strong group and never lie down. When the chips have been down and everyone thought we had no right to win games, we come out and win games.
“This group will pick itself up and I will give them loads of positives. This is a setback but the group couldn’t help what has been done.”
Asked about Scunthorpe’s decision to play a largely unrecognisable team against Rovers, Brady said: “It doesn’t concern me, we need to look forward as a group. Whatever is done is done, whether it is right or wrong.”
But he added: “Barrow played a full-strength side. They are a good team.
“No team since Phil Brown took over has gone 3-0 up here, no team has won here.
“But I don’t need picking up, we will be up for it.”
Barrow have lost six of Brown’s nine games in charge, but key wins over Sutton and champions Forest Green paved the way for their survival in League Two for a second season.
Brown has held talks about an extended deal and looks set to remain in charge next term.
“It is not over the line yet,” he said. “Would I like to be here next season? Absolutely. I have enjoyed my time here and the support I have received from the board and the fans has been nothing short of brilliant.”
Chairman Paul Hornby said the two parties were “close” to agreeing terms.
Brown added: “There’s almost an agreement in principle from negotiations on Friday which went on into the late hours.
“That didn’t take my mind off the game. I had done my work and hoped the players would carry out what we had set out for them.
“So it was disappointing in the first half. We looked devoid of any information we had spoken about.
“It looked like we had lead boots on in the first half and hadn’t played together before. It was too far off the mark, though, we raised a gallop in the second half.
On Northampton’s heartbreak, Brown added: “It beggars belief. I can’t but help feel for their manager and I wish them all the best in the play-offs. It just doesn’t feel right.”