It was Southend who nearly opened the scoring when striker Scott Vernon’s close-range shot was brilliantly saved by Willy Gueret.
The Dons then hit back and went ahead when Jermaine Easter cut the ball back for Mark Carrington to slot low past keeper Steve Mildenhall from 12 yards.
Simon Francis struck the post for the Shrimpers, but the home side were able to double their advantage when Carrington controlled Dean Lewington’s low cross and rifled a precise left-foot shot into the corner for his fourth goal of the season.
Steve Tilson’s men continued to plug away and Vernon nearly dragged the visitors back into the match, before Andros Townsend sealed the win for the Dons with 10 minutes remaining.
Sub Matthew Paterson pulled one back at the death for Southend, but the points belonged to Paul Ince’s side.