Winger Paul Warne put the visitors in front with just 10 minutes left on the clock.
But two minutes into injury time Southend striker Lawrie Dudfield had the ball in the back of the net only for his effort to be ruled out for offside.
The Nottinghamshire visitors started the brighter of the two sides with striker Derek Asamoah being denied by a Bart Griemink save after five minutes.
Five minutes later the forward's 25-yard snap shot went yards wide as Southend struggled to get into game.
The fourth-placed Shrimpers finally got going when central midfielder Mark Bentley headed wide from eight yards, before seeing his awkward shot from Andy Edwards' knock down held by Kevin Pilkington in the Town goal.
Mansfield then struggled to keep the ball in midfield and had to be grateful to their defence for keeping the Shrimpers at bay.
The second half started much the same as the first with Asamoah being denied by Griemink twice in the first five minutes.
And it was Asamoah who nearly opened the scoring when he collected Joel Kitamirike's cross but saw his shot deflected over.
But the Stags finally made the breakthrough on 79 minutes when Asamoah cut inside for Tom Curtis to set up the unmarked Warne, who side-footed home.
Southend had chances from Bentley and Adam Barrett before the Shrimpers' claims for a penalty for handball in the dying minutes were waved away by referee Paul Robinson.
And after Asamoah fired another attempt over the bar came that injury time scramble in the Mansfield box.
Wayne Gray's header was cleared off the line by Luke Dimech, before Dudfield's follow up was ruled out for offside.