Dougie Freedman's second-half header earned Southend their first league victory since Boxing Day.
The 34-year-old latched on to a pass from debutant defender Dorian Dervite and looped the ball over keeper Steve Phillips before heading in from a yard.
Phillips was lucky to only receive a booking shortly after when he handled a shot from the striker outside the box.
Darryl Duffy missed a chance to level when he broke clear, only for Southend keeper Steve Mildenhall to save.
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