Fleetwood’s relegation to League Two was confirmed despite their late 1-0 away victory against Leyton Orient.
Xavier Simons scored the only goal of the game three minutes into added time to secure victory for the visitors.
But Burton's win at home to Reading sealed Fleetwood's fate.
In a match of endeavour but lacking quality, Town almost took the lead early in the second half when a bullet header by Carl Johnston was punched clear by goalkeeper Sol Brynn from point-blank range.
The Orient keeper was soon extended again to keep out a Ryan Broom effort.
But Jay Lynch was the busier of the two keepers in the first half. He was fully extended when he tipped a 22-yard free-kick by Tom James over the bar and then pushing away a powerful drive by Ethan Galbraith.
Brendan Sarpong-Wiredu went on an enterprising run before his effort was collected by Brynn as Fleetwood pushed for a second-half winner.
It arrived when Simons collected a pass from Tommy Lonergan after Orient failed to clear their lines and neatly struck the ball past Brynn.
But it was not enough to take Fleetwood's fight to the last weekend of the season.
Adam eyes instant Fleetwood return
Fleetwood boss Charlie Adam:
"It's been a tough day for everybody involved at this football club, the directors, the management the players and the supporters.
"That group of players have given us everything since we came in on December 31 and it's unfortunate that we've just come up short. It really is bitterly disappointing for Fleetwood as a club and for the town.
"I thought we were in full control of the game, we were never really under pressure and that's what you will see from this side next season. They are going to run and fight all the way.
"That performance away from home was very good. I can't thank the supporters enough for coming to support us. They have been with us all season since we came into the building and I'm really gutted for them.
"There is a lot of frustration of why and what but we'll sit down and address things and we are going to do everything we can to come straight back up. We have the nucleus of a very good squad in League Two because they've shown they are good League One players.
"I'm already thinking about next season, what we want, what we need, how we are going to play and what we are going to do."