By John Burgum
Their 14,000 fans, outnumbered 2-1, had also left - silenced for the only time in a match which produced a record gate for a Third Division play-off final.
Minutes earlier they were in full voice anticipating, along with everyone else, that a tense contest which produced so few scoring opportunities was destined for extra time - possibly even penalties.
But as Keith Walker lunged at Christian Lee, there was one last cruel twist to a season which literally went down to the final kick.
Swansea hearts probably missed a beat as Northampton won a free-kick in an inviting position outside the box and directly in front of goal. Even the players feared the worst: "When you concede a free-kick on the edge of the area at any time in the game you know the opposition are capable of scoring because so many teams these days are good at set pieces," admitted skipper David Penney.
It was the third minute of stoppage time. Thirty four seconds later John Frain drove the twice-taken free kick into the back of the net to break Swansea hearts and end the club's bold bid to claim the last promotion spot. It was a sad, rather controversial end to a campaign which had promised so much after that autumn of despair.
Not even the dubious time-keeping of referee Terry Heilbron nor the complaints which followed Jonathan Coates' booking for charging down Frain's first attempt could ease the pain. The Northampton defender made no mistake a second time.
As a colleague enticed Penney to open a gap in the defensive wall Frain exploited it with a perfectly driven left foot shot.
"That was the most important goal I've ever scored," said the full-back who was a Birmingham reserve six months ago.
There was barely time to restart a poor quality match which had begun so promisingly when Carl Heggs forced a brilliant save from Andy Woodman.
But for all the possession Swansea enjoyed, particularly in the second-half, they never conjured a better scoring opportunity. There were half chances, the odd near miss but the match was often bogged down in midfield and dominated by two tight defences.
It cried out for width to stretch defenders. Wembley is made for an expansive game, but tight marking and the absence of quality wingers, meant neither side was able to widen its repertoire.
Swansea realised that when they drafted on Linton Brown, but his introduction, clearly with one eye on extra time, came too late to have any impact.
"I felt we were the better side throughout, but sometimes you can dominate games too much," insisted Molby. "I think we lost some of the urgency in our play. We never made it a real stamina test. Had it been, I think we would have come out on top."
The manager added: "If it had gone to extra time I felt if we kept creating, kept pumping crosses into the box with tired legs we might just pop one in. That's what happened, but at the wrong end and at the wrong time."
Northampton were just as bereft of creativity in front of goal. Roger Freestone never had a shot to save and, on the only time he was beaten, when Paul Grayson robbed Molby and invited would-be Welsh International Sean Parrish to drive across the face of the goal, the back-tracking Christian Edwards cleared off the line.
Edwards hardly put a foot wrong - winning his physical contest hands down with the cumbersome John Gayle. There were telling contributions, too, from Walker and Kwame Ampadu who worked tirelessly in midfield.
Penney, out of position at full-back, kept a tight rein on the elusive Grayson, but Swansea certainly missed his driving runs down the middle. What Swansea also lacked was a player capable of delivering those pin-point crosses which defenders hate when facing their own goal. Molby delivered one or two teasing examples, but there were no Wembley smiles from the manager on probably his final appearance in front of the Twin Towers.
Twelve months down the line it might be different, and Swansea fans will be hoping that that rendition of Move It On Up was merely a rehearsal for next season's automatic promotion bid.
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