David Martin and Neil Harris scored the goals to pile the pressure on Burton boss Paul Peschisolido, whose side have now gone 11 games without a win.
Southend keeper Dale Belford had a busy first half in his first appearance on loan from Bury. He had a lucky break when Brewers striker Adi Yussuf squandered a great chance in the third minute, but later showed a safe pair of hands as Cleveland Taylor, Jimmy Phillips and Aaron Webster tried to break the first-half stalemate.
Southend axed four players from their matchday squad for club disciplinary reasons, including top scorers Liam Dickinson and Ryan Hall.
Veteran striker Harris had chances to give them the lead, but headed too high from a corner before he was denied by Ross Atkins’ full-length save.
Southend, who had lost their last two, made the stronger start to the second half and Martin gave them the lead on the hour mark when he beat Atkins with a quickly-taken free kick from 25 yards. And the visitors sealed victory when Harris hammered home the rebound after Atkins had done well to keep out Anthony Grant’s shot in the 75th minute.