Southend United striker Barry Corr hit his first goals since the first day of the season to wreck Fleetwood's hopes of returning to the top of League Two.
Corr headed the Shrimpers in front on 21 minutes from Kevan Hurst's cross.
The home side then sealed the points with an 81st-minute penalty.
Stewart Murdoch was adjudged to have fouled Will Atkinson and Corr powered his spot-kick into the top-left corner to confirm the hosts' third straight league win.
Fleetwood had been on top up until the Shrimpers' first goal, striker David Bell having had two low shots saved by Southend keeper Daniel Bentley, who also did well to parry a well-struck shot from Antoni Sarcevic.
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