Morecambe have now not been beaten in any of the six meetings between the two sides.
And it was Fleming's determination in the 34th minute which swung the latest match in favour of the visitors.
Fleming won the ball off Southend right back Sean Clohessy as he attempted to usher the ball out of play before rolling a low, 10-yard shot in to the back of the net.
Up until that point the home side had been on top with Ryan Cresswell heading a right-wing free-kick from Freddy Eastwood inches over the crossbar.
Shrimpers striker Gavin Tomlin also had an effort impressively saved by Morecambe goalkeeper Barry Roche before Barry Corr fired over from close range after being teed up by Kevan Hurst.