Adam McGurk's goal separated the sides after the first leg and Burton doubled their advantage early on through Marcus Holness, only for Phil Brown's Shrimpers to hit back through Ryan Leonard and Anthony Straker.
But former Aston Villa youngster McGurk slammed in his 12th goal of the season midway through the second half to make it 2-2 on the day and secure a 3-2 aggregate win and a final date with Fleetwood a week on Monday.
Southend were desperate for an early goal and almost grabbed one in the opening moments but Burton goalkeeper Dean Lyness tipped Kevan Hurst's piledriver over the crossbar.
Instead it was Burton who drew first blood to double their lead in the tie after 21 minutes when Chris Hussey swung in a free-kick and Holness was left unmarked at the far post to power his header past home goalkeeper Daniel Bentley.
However, Southend hauled themselves back into it just after the half-hour mark with a spectacular strike from Leonard.
When Burton half-cleared a corner, Ben Coker hooked the ball back in to Leonard, who swivelled and thumped a volley over his shoulder from the edge of the area.
Burton's intentions became clear as the interval approached with Hussey booked for time-wasting with just 39 minutes on the clock.
The tactic did not work, though, as moments later United levelled the tie when David Gray dawdled on the ball 30 yards out and promptly lost possession.
Michael Timlin swung in a deep cross and Straker charged in at the back post to meet it with a firm downward header past Lyness.
Leonard almost doubled his tally seconds after half-time when he charged down the left and struck a fierce, angled drive which Lyness blocked at his near post.
At the other end Burton sub Billy Kee saw his deflected shot saved before the visitors grabbed the lead back in the 69th minute.
Southend failed to deal with another Hussey free-kick and the ball ricocheted to the feet of McGurk, who was able to turn and sweep the ball past the advancing Bentley.
Brown threw on home hero Freddy Eastwood in a bid to salvage the tie, and Bentley spent much of the last five minutes playing in the opposition penalty area.
But Burton, beaten at this stage last season, withstood the late barrage to go one step further this time around and keep alive their dream of a first-ever promotion to League One.