League Two leaders Burton overcame the dismissal of Robbie Weir to hit an 89th-minute winner through Nasser El Khayati and go five points clear.
Jon McLaughlin saved Barry Corr's penalty after he was fouled by John Mousinho. But Corr then made amends to put Southend ahead before the break.
Weir was sent off after a clash with Corr, but 10-man Burton levelled through Matty Palmer's 18-yard shot.
El Khayati then earned a third straight win when he fired into the far corner.
Hasselbaink hails '100-man' Burton
Burton Albion manager Jimmy Floyd Hasselbaink told BBC Radio Derby:
"We were organised and hard to beat but, when we had the ball, we passed it. We passed it in the way they could not touch it, even when we had 10 men.
"It was always going to be a counter-attacking game and we did that really, really well. We went forward and caused them big problems.
"I am convinced we deserved to win. You could see the togetherness in the second half."
- Published20 June 2016
- Published7 June 2019
