A dull game burst into life in the last 20 minutes when Harriers managed to secure the three points with improved attacking and some good goalkeeping from Fraser Digby.
On-loan John Melligan's 10th goal of the season, a clever lob, was enough for Harriers to once again revive their play-off hopes.
But Digby then had to save smartly from Daniel Marney's low shot and Tes Bramble's vicious volley.
Substitute Sean Parrish blocked a Leon Cort header on the line three minutes from time as the match sprung into an end-to-end affair in the latter stages.
Southend keeper Aaron Flahavan replied with two good saves from the inspired Melligan.
But it was Harriers who took the vital points which will set them up well for Saturday's trip to Rochdale.
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