Paul Sturrock's men had not lost in 14 outings in a run stretching back to October 23, but Burton improved their own promotion hopes with their second home win in four days.
The hosts made a bright start and were rewarded with the opening goal in the 16th minute when Calvin Zola slid home a Lee Bell cross from six yards for his 11th goal of the season.
Southend enjoyed a spell of domination during which top scorer Gavin Tomlin had a shot pushed round a post by home 'keeper Dean Lyness.
Burton survived a searching examination to double their advantage in the 36th minute.
Zola played the ball across the edge of the area and Bell's fierce shot took a big deflection off Southend skipper Paul Smith to leave keeper Paul Smith stranded.
Lyness was able to smother a deflected Michael Timlin free-kick as the visitors tried to find a way back into the game after the break.
Burton had defender Nathan Stanton sent off for a second yellow card after a clash with Luke Prosser in the 75th minute.
