The visitors' boss Liam Watson, who had seen his side suffer seven successive defeats, changed his tactics to five across the box and it paid off.
Morecambe dominated the game but struggled to create clear chances and when they did came up against an excellent Steve Dickinson.
The first half was a bland affair with few chances.
Morecambe had the majority of the possession, but struggled to break down a Southport side who looked far more solid than they had a week when they went down 3-0 to the Shrimps a week earlier.
Both sides tested the waters with efforts from distance in the early stages. Ged Brannan flashed two shots wide for the home side in the first ten minutes before Michael Powell tried a similar effort moments later.
Brannan was to be Morecambe's biggest influence in the first half and he came close to forging the game's opening goal on 24 minutes with an excellent run and cross from the byline. Danny Carlton reacted well to meet the ball at the near post, but was denied by Dickinson.
The excellent Southport keeper was certainly busy in the second half with good saves from a Michael Twiss header and a Jimmy Kelly free-kick but he should have been beaten in the 64th minute.
Great work from Carlton saw Twiss presented with the easiest of opportunities, but the home side's top scorer blasted the ball well over the bar from six yards out when it looked easier to score.
The ever dangerous Garry Thompson flashed a shot across the goal and Carlton's overhead kick missed the target by inches, before the visitors almost scored themselves with a late break.
Skipper Steve Pickford made a good break from midfield and set himself up with a neat bit of skill, but dragged his effort wide of the left-hand post.