An own goal from Southend centre back Luke Prosser ended up giving the Brewers another important three points to send Jimmy Floyd Hasselbaink's three points clear at the top of Sky Bet League One once more.
The deciding moment came just over five minutes into the second period when Tom Naylor picked up a loose ball just outside the box and fired on goal. The former Derby man is yet to score in a Burton shirt and in all fairness this effort was going just off target until it hit the legs of Prosser leaving visiting goalkeeper Daniel Bentley beaten all ends up and unable to keep the ball out.
In truth there were not many clear cut chances in the game, Southend's best chance coming when Albion skipper John Mousinho diverted a low cross towards his own goal, Jon McLaughlin making an excellent reaction save to keep the scores level, as it was at that stage of the game in the first half.
Naylor was one of two changes to the side that ground out a very creditable point against Sheffield United on Tuesday. Calum Butcher was the man who made way, maybe a cautious move from the Brewers boss, with his central midfielder currently sitting on four yellow cards. Lucas Akins returned to the side in place of Jerome Binnom-Williams who had to settle for a place on the bench against the club he spent a large part of last season with in a loan spell.
The early probings of Naylor almost opened up Southend on seven minutes, an excellent ball inside full back Ben Coker picking out Phil Edwards whose teasing low cross just eluded both Stuart Beavon and Nasser El Khayati in the middle. El Khayati quickly had a chance on the edge of the box switching the ball from right foot to left and hitting a deflected shot that allowed Albion to keep the Southend goal under siege with a corner.
Anthony O'Connor, forward to support set pieces was needlessly bundled over by the touchline giving Mark Duffy chance to swing in a teasing centre but with everyone sucked into the centre of the six yard box the Birmingham loanee overhit his free kick beyond the back post.
Visiting skipper Michael Timlin will doubtless feel he should have done better when a headed clearance from Mousinho landed at his feet but as Albion defenders rushed out he blazed well over the bar.
Albion soon resumed their ascendency with excellent link up from Akins and Beavon opening up a chance for Duffy to run onto the latter's cushioned header and send a rising drive just over the frame of the Southend goal thanks to the fingertips of the highly regarded Shrimpers keeper.
Duffy then turned provider with an inch perfect cross to Mousinho who fluffed his lines with a header wide from six yards out.
Southend did have chances, David Worrall providing David Mooney the chance to set up Joe Pigott who was quickly crowded out.
McLaughlin then came to Albion's rescue saving Mousinho's skewed clearance before referee Trevor Kettle showed his first yellow card of the afternoon, Robbie Weir the first man into the book for what looked like a 50-50 challenge with Ryan Leonard near the half way line. Mr Kettle saw it differently and booked the Albion midfielder.
Albion were forced into a change just after the half hour mark. El Khayati had been struggling somewhat after an early challenge from Timlin and Matty Palmer was introduced in a straight swap in the attacking three behind Beavon.
The game was meandering to half time as both sides continued to frustrate and carving out very little in the way of clear chances.
Half time: Burton Albion 0-0 Southend United
It seemed that Albion's half time team talk was the more inspirational, the Brewers coming out a lot more purposeful from the restart. Palmer saw a deflected effort trickle just wide of the upright before O'Connor, up for a corner, got his feet in a tangle inside the box and was unable to get a shot away inside the box. The ball came out to Duffy who rippled the side netting as the ball came loose.
The deadlock was finally broken when Duffy swung a corner over and this time Naylor put his foot through the ball forcing PROSSER to turn the ball home.
Duffy almost immediately curled a right footer over the bar as Albion looked to put clear daylight between the sides but it was Prosser who went closest to the next goal heading wide under pressure from Mousinho.
Palmer fired over after a short corner routine with Duffy before Southend went route one and almost caught the Brewers out. Bentley launched a long kick straight down the middle and Pigott was there first attempting a lob over McLaughlin who did well to come off his line quickly and snuff out the chance.
Duffy forced Bentley to show good hands with a shot straight at the keeper before substitute Anthony Wordsworth followed Weir into the book for clipping the heels of Akins as the Burton man burst into the Southend half.
Another Southend substitute Myles Weston had pace to burn down the left and his cross was headed straight at McLaughlin by Mooney and the same combination were involved as the substitute burst from half way with an angled run, delivering the ball across the box but ex-Orient striker Mooney could not quite get there to turn it home.
Leonard was carded for a foul on Weir, similar to the one that saw Weir go in the book on the same player and Damien McCrory was also harshly carded for feinting to take a free kick late on, Mr Kettle seeing it as timewasting. It mattered little as Albion were good value for the points on a day when flowing football was not seen in great amounts but Albion showed their gritty side to get the job done.