The Grecians went in front in the 17th minute when the recalled Troy Archibald-Henville played the ball through for Adam Stansfield who took full advantage of Steve Mildenhall’s indecisiveness by lofting the ball over the Southend goalkeeper and in off the far post.
Southend had chances themselves with Jabo Ibehre heading wide from six yards with the score goalless and doing the same again shortly after Exeter’s opener.
Southend were the better of the two teams in the second half, but never really troubled Exeter goalkeeper Paul Jones.
The Grecians were reduced to ten men shortly after the hour mark when Barry Corr was sent off for an off the ball incident and Southend also had a man dismissed when Ibehre saw red after clashing with Richard Duffy.
Stansfield had a great chance to wrap things up for Exeter, but he fired wide when through on goal.