Southend revived their hopes of automatic promotion and left Burton without a win in 11 games.
The Shrimpers dropped four players from their side for breaching club discipline, including top scorers Liam Dickinson and Ryan Hall.
Adi Yussuf wasted a great chance for the Brewers before David Martin netted a quickly-taken free-kick for Southend.
They made sure of the points when Neil Harris hammered home the rebound after Anthony Grant's shot was saved.
VIEWS FROM THE DRESSING ROOM
Burton boss Paul Peschisolido told BBC Radio Derby:
"It's now 11 games in a row. I don't know where that puts me. We'll see.
"We went into Christmas in top form, fourth in the table and now it's 11 games without a win. I can't believe it's the same group of players.
"We're very fragile at the moment; we had enough chances to score one or two goals in the first half and if you don't score when you're in that fragile state, you're always liable to concede one."
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