A late Mark Phillips header secured the points for 10-man Southend against Gillingham.
Defender Phillips headed home Ryan Hall's corner three minutes from time.
Earlier the Shrimpers hit the bar through Blair Sturrock before Bilel Mohsni was sent off after a yellow card for a foul and another for dissent.
Luke Rooney was twice denied by Glenn Morris, who also saved well from Danny Kedwell and Stefan Payne as Southend held on.
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Southend manager Paul Sturrock told BBC Essex:
"I think he [Mohsni] brings a lot of it on himself, I must admit.
"His dramatics are beginning to become well-known by referees and he's not helping himself in any form.
"The second one [yellow card] was unbelieveable, he's put his hands up to get out of the road and the boy kicks the ball off him, there was no way it was a yellow card."