Ajay Leitch-Smith and Max Clayton added to Adam Dugdale's first-leg winner to ensure a Wembley appearance for Steve Davis' men against either Torquay or Cheltenham.
Substitute Neil Harris and Chris Barker responded for Southend after the break, but despite their best efforts, the home side were unable to snatch the crucial goal to take the match to extra-time.
The early stages of the first-half had an edgy feel about them and it wasn't until Leitch-Smith opened the scoring that the game sprung into life. With 24 minutes on the clock, the highly-rated striker latched onto Ashley Westwood's through ball, before cutting inside of his marker Sean Clohessy and driving his shot into the bottom right-hand corner.
Seven minutes later, Freddy Eastwood thought he had brought Southend back onto level terms but his goal was correctly ruled out for offside. Crewe stopper Steve Phillips could only parry Ryan Hall's bending effort and even though Eastwood was the first to react, the linesman swiftly raised his flag.
Byron Moore should have made it 2-0 to Crewe on the night in the 34th minute when Southend goalkeeper Cameron Belford scuffed a routine clearance. The midfielder had time to steady himself in the penalty area but he somehow blazed his shot high and wide under minimal pressure.
The ever-dangerous Leitch-Smith soon found himself through on goal once more when Lee Bell poked a ball over the Southend defence, but having chested it down, the 22-year-old failed in his bid to lift the ball over the oncoming goalkeeper.
Shortly after the restart, Moore attempted to make amends for his glaring miss by teeing himself up for a stinging volley which Belford was equal to.
Having failed to establish a foothold in the game, Southend were desperate for a sign of encouragement. In the 53rd minute, Michael Timlin provided the necessary tonic as his left-footed effort rattled Phillips' right-hand post.
Eastwood went just as close moments later but his attempt ricocheted off the inside of the other post and agonisingly flashed across the goal to safety.
An equaliser seemed inevitable and there were no surprises when it finally came. Phillips and his defence failed to deal with Barker's delivery from the right and the ball eventually fell to the feet of Harris who tapped into a gaping goal.
With confidence running high, Bilel Mohsni had a free-header to level the scores on aggregate but his effort went straight into the hands of a grateful Phillips.
Crewe's 17-year-old forward Clayton - on as a substitute for Leitch-Smith - promptly went up the other end and effectively ended the tie as a contest. Having got himself on the ball near Southend's by-line, the youngster slowly eased his way inside before sneakily placing a shot through the legs of defender Luke Prosser and past a helpless Belford at his near post.
Southend weren't going to go down without a fight and although Barker's late headed goal gave them a lifeline, they couldn't manage to fathom the all important leveller.
Southend United: Belford, Clohessy, Gilbert (Hills 32), Mohsni, Prosser, Barker, Hall, Grant, Timlin, Benyon (Harris 54), Eastwood. Subs: Morris, Ferdinand, Hills, Martin, Harris.Goals: Harris (64) and Barker (88).
Bookings: Grant (74).
Red cards: N/A
Crewe Alexandra: Phillips, Tootle, Davis, Artell, Dugdale, Westwood, Bell, Mellor, Leitch-Smith (Clayton 75), Moore, Powell. Subs: Martin, Shelley, Martin, Bodin, Clayton.
Goals: Leitch-Smith (24) and Clayton (86).
Bookings: Leitch-Smith (36), Davis (63) and Powell (70).
Red cards: N/A
Referee: Darren Drysdale (England)