Goals from Barry Corr, Marc Laird and Freddy Eastwood saw the Shrimpers come out on top.
They went in front in the 33rd minute when Michael Timlin's diagonal pass was headed back across goal by Chris Barker and Barry Corr, who was making his first start since April 2011, nodded in from six yards.
Stockport started the second half brightly but found it hard to create goalscoring chances and Southend took full advantage by doubling their lead in the 85th minute .
Timlin was again involved as his delivered a low left wing cross which picked out Laird and the on loan Leyton Orient midfielder fired into the bottom left hand corner of the net from six yards.
The Shrimpers then made sure of the victory three minutes later when substitute Eastwood blasted the ball in to the roof of the net from just inside the penalty area.