Keenan Appiah-Forson headed the only goal of the game early on as the Shrimpers hit back from last week's heavy defeat at Boston to keep their promotion hopes alive.
Appiah-Forson reacted fastest when Latics' 'keeper Tom Donaghy parried an initial effort from Leon Chambers-Parillon, knocking the ball home from point-blank range.
Southend continued to have the better chances with Macauley Bonne bringing another save out of Donaghy and Noor Husin firing over the crossbar, but the hosts had done enough to bring Micky Mellon's side's five-game unbeaten run to an end.
Boss Mellon said: "We gave away, from our point of view, a poor goal from a breakaway and we can be a bit more aggressive in dealing with the save the goalkeeper makes.
"But in the second half we showed much, much more."
Latics' next fixture is on Tuesday week, April 8, when they host Woking.
