Southend's victory hopes at Wembley have ended in defeat.
Early goals in each half from Luke Murphy and Max Clayton were enough for Crewe to win the Johnstone's Paint Trophy for the second successive season.
A superb strike from Murphy opened the scoring after six minutes and the League One side threatened to run riot in a rampant opening quarter of an hour.
But Southend imposed their physicality to work a way into the contest and Tamika Mkandawire passed up a glorious headed opportunity to level matters before half-time.
Shrimpers fans celebrated what they thought was the award of a penalty before the half hour when Britt Assombalonga tangled with Railwaymen defender Mark Ellis. Referee Nigel Miller correctly signalled for a goal-kick.
The Blues were by now asking regular questions of Crewe and should have been level nine minute before the break, but Mkandawire sent a free header over from Barker's corner.
That momentum was spurned early in the second half as Southend gifted Crewe their second.
Ryan Creswell played the ball into midfield when Mohsni was slow to react and bundled aside by Murphy before Chuks Aneke and Moore combined to leave Clayton with a tap-in.