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.
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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."