Nile Ranger was involved in the first meaningful chance as his neat flick found Anthony Wordsworth on the edge of the box, but the midfielder's low shot was well saved by James Shea.
Ranger then got a brilliant opener for Southend in the 35th minute, shuffling past three players and prodding a shot into the right-hand corner while off balance to score his third goal in as many games.
The Dons had been wasteful in possession but Lyle Taylor nearly latched onto Tom Soares' through-ball just before half-time.
Simon Cox doubled Southend's lead shortly after the hour mark after taking advantage of a fortunate rebound in midfield and lashing past Shea from 20 yards.
Shrimpers substitute Theo Robinson hit the post after latching on to a ball over the top, but the away side were rarely troubled at the other end as they maintained their play-off hopes.
Match report supplied by the Press Association.
Match ends, AFC Wimbledon 0, Southend United 2.
Second Half ends, AFC Wimbledon 0, Southend United 2.
Foul by Darius Charles (AFC Wimbledon).
(Southend United) wins a free kick in the attacking half.
Dean Parrett (AFC Wimbledon) wins a free kick in the attacking half.
Foul by Theo Robinson (Southend United).
Will Nightingale (AFC Wimbledon) wins a free kick on the left wing.
Foul by Nile Ranger (Southend United).
Attempt blocked. Darius Charles (AFC Wimbledon) right footed shot from the left side of the six yard box is blocked.
Foul by Andy Barcham (AFC Wimbledon).
Will Atkinson (Southend United) wins a free kick in the defensive half.
Paul Robinson (AFC Wimbledon) wins a free kick in the defensive half.
Foul by Nile Ranger (Southend United).
Substitution, AFC Wimbledon. Dominic Poleon replaces Lyle Taylor.
Substitution, AFC Wimbledon. Tyrone Barnett replaces Tom Elliott.
Corner,  Southend United. Conceded by Darius Charles.
Theo Robinson (Southend United) hits the right post with a right footed shot from the centre of the box.
Substitution, Southend United. Theo Robinson replaces Simon Cox.
Delay over. They are ready to continue.
Delay in match Simon Cox (Southend United) because of an injury.
Lyle Taylor (AFC Wimbledon) is shown the yellow card.
Attempt blocked. Dean Parrett (AFC Wimbledon) right footed shot from outside the box is blocked.
Delay in match Andy Barcham (AFC Wimbledon) because of an injury.
Corner,  AFC Wimbledon. Conceded by Jason Demetriou.
Substitution, AFC Wimbledon. Dean Parrett replaces Tom Soares.
Attempt missed. Lyle Taylor (AFC Wimbledon) left footed shot from outside the box is close, but misses to the left.
Goal!  AFC Wimbledon 0, Southend United 2. Simon Cox (Southend United) right footed shot from the centre of the box to the top right corner.
Corner,  AFC Wimbledon. Conceded by Anton Ferdinand.
Attempt missed. Jake Reeves (AFC Wimbledon) right footed shot from outside the box misses to the left.
Will Nightingale (AFC Wimbledon) wins a free kick on the left wing.
Foul by Ben Coker (Southend United).
Corner,  Southend United. Conceded by James Shea.
Attempt saved. Will Atkinson (Southend United) left footed shot from the right side of the box is saved in the bottom left corner.
Foul by Tom Soares (AFC Wimbledon).
Anthony Wordsworth (Southend United) wins a free kick in the defensive half.
Attempt missed. Tom Elliott (AFC Wimbledon) left footed shot from the left side of the box is close, but misses to the right.
Second Half begins AFC Wimbledon 0, Southend United 1.
First Half ends, AFC Wimbledon 0, Southend United 1.
Foul by Tom Soares (AFC Wimbledon).
Anthony Wordsworth (Southend United) wins a free kick in the defensive half.
Phil Brown marked his fourth anniversary in charge of Southend with a third consecutive win as his side beat Wimbledon in League One.