Phil Brown's side enjoyed a dream start with two goals in the opening nine minutes and never looked in any danger after that in what was their seventh meeting with the Shrimps.
The first came after seven minutes as the impressive Kevan Hurst crossed from the right for Anthony Straker to bundle the ball home from close range at the far post.
Just minutes later it was two-nil as Straker added his and Southend's second. The wide man cut in from the left and let fly with a right-footed shot which took a wicked defelection off a Morecambe defender to divert the ball past the flat-footed Barry Roche.
Morecambe looked to get back in the game but, with Southend defending superbly, rarely threatened.
Andy Wright directed a near-post header from a Ryan Williams corner inches wide of a post and Chris McCready missed a golden chance in the second half when he blazed over from close range.
Ryan Leonard then capped off a fine afternoon for the visitors with a third goal deep into injury time, beating Roche low to his right with an effort from distance.