After a goalless first half, the deadlock was broken in the 75th minute after an error from Burton's goalkeeper Dean Lyness who failed to stop Antoni Sarcevic's long-range free kick.
Fleetwood Town finished five points behind Rochdale and Scunthorpe United (who were promoted in third and second place respectively), and eight behind league winners Chesterfield.
Adam McGurk put the home side ahead just before half-time as he lobbed the Southend goalkeeper Dan Bentley.
On the hour mark, Ian Sharps was dismissed after being shown a second yellow card, forcing Burton to play the last 30 minutes with ten men.
Midway through the first half, Burton extended their aggregate lead when Marcus Holness scored with a header from a Chris Hussey free kick.
Ryan Leonard then reduced the deficit with an overhead kick before Anthony Straker's headed goal made it 2–1 to Southend at half-time.
McGurk scored from a Hussey free kick midway through the second half to make it 2–2 on the day, with Burton progressing to the final with a 3–2 aggregate victory.
Five minutes after half-time Matty Blair put Fleetwood ahead from close range after Antoni Sarcevic had seen his shot blocked on the line.
The home goalkeeper Chris Maxwell made saves from both Michael Coulson and Keith Lowe while Nick Pope, his opposite number, denied Sarcevic.
The teams were also drawn against one another in the second round of the 2013–14 FA Cup: the tie, played in Fleetwood in December 2013, was a 1–1, with Burton winning the replay 1–0 ten days later.
[13] Burton, who wore yellow and black kit, adopted a 4–4–2 formation while Fleetwood, in red and white, played as a 4–4–2 diamond.
Within a minute, a high free kick from McGurk found Kee in the Fleetwood penalty area but his header was saved by Maxwell.
In the 64th minute, Burton made the first substitution of the game with Zander Diamond coming on to replace Holness who appeared to be suffering from a hamstring injury.
With fifteen minutes of the game remaining, Fleetwood took the lead: Lyness came out to punch clear Sarcevic's 35-yard (32 m) free kick but the ball flew over the goalkeeper and into the Burton goal.
[15] His opposite number Gary Rowett noted that "I wanted the players to watch Fleetwood pick up the trophy so they felt the hurt.