Man of the moment Jack Redshaw scored his third goal in two games to give Morecambe a third win in four league games.
The tiny front man, who is beginning to make a big name for himself, produced a clinical finish two minutes from time to give Jim Bentley’s side another excellent win.
It was Redshaw’s sixth goal of the season and the best moment of a game dominated by both defences.
Southend had the first effort of note when former Morecambe loanee Ryan Cresswell headed over a Kevan Hurst corner from close range.
Morecambe hit back with Kevin Ellison curling an effort wide from the edge of the box and Redshaw almost surprising Paul Smith with a long-range shot.
Britt Assombalonga, the visitors’ danger man with nine goals in 12 games coming into the match, showed what he can do on 20 minutes with a storming run into the box but dragged his final shot wide of the right-hand post.
Defenders then protected their respective goalkeepers for the remainder of the half with superb blocks at both ends.
Anthony Straker foiled Shrimps’ Lewis Alessandra, with Nick Fenton and Stewart Drummond putting their bodies on the line to divert shots.
The Shrimps dominated the second half and created a host of half-chances. Redshaw just failed to get the finishing touch to an Ellison header back across goal and Redshaw also drilled a shot wide after a lovely first touch from Jordan Mustoe’s clever through ball.
Fenton found himself with a rare chance on 65 minutes but he was unable to get the ball under control.
After being second best for long periods Southend had a great chance to open the scoring five minutes from time when Ryan Leonard’s cross found Johnson Clarke-Harris five yards out.
But the substitute could only scuff his shot and Fenton was able to clear off the line.
Morecambe finally got a deserved goal two minutes from time when Redshaw took full advantage of good work from Ellison and substitute Richard Brodie to lash home the loose ball from 12 yards.
There was more drama to come with the Shrimps reduced to 10 men on 90 minutes when Brodie tussled with Sean Clohessy, and saw a straight red.
He was almost made to pay for his ill discipline when Hurst curled an effort just over but the Shrimps hung on.