Steve Davis' men triumphed by the same scoreline in last term's npower League Two play off-final against Cheltenham and they overcame a Southend side who battled gamely for revenge having been Alex's semi-final victims 11 months ago.
A superb strike from Railwaymen captain Murphy opened the scoring after six minutes and the League One side threatened to run riot in a rampant opening quarter of an hour. Crewe added a second through Clayton's close-range finish in the 49th minute after some slack Blues defending.
Bilel Mohsni claimed he was fouled by Murphy in the build up to the second goal and the enigmatic forward almost reduced the arrears shortly afterwards, but the Shrimpers were to to bridesmaids in this competition once more as in the 2004 and 2005 finals.
The opening goal arrived in some style. Byron Moore's corner from the right was stroked low towards the edge of the area from the right and Harry Davis dummied the pass for Murphy to steer into the top corner despite Anthony Straker's presence on the goal-line.
Moments later the whole ground stood and applauded in a pre-planned tribute to the family of absent Crewe defender Adam Dugdale, whose newborn son sadly passed away at the end of the week.
Shrimpers fans celebrated what they thought was the award of a penalty before the half hour when Britt Assombalonga tangled with 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 minutes before the break, but Tamika Mkandawire sent a free header over from Chris 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.
Mohsni immediately looked to make amends but his header from point-blank range was superbly diverted away from the goalmouth by Davis. Boss Phil Brown brought on Ben Reeves and Barry Corr for Barker and Mohsni before the hour and Corr headed wide when his fellow substitute played in Gavin Tomlin to cross.
In the 73rd minute, Corr saw his header from Reeves' corner hacked off the line by Matt Tootle after Kelvin Mellor deflected his initial strike behind. Southend's efforts took their toll and Paul Smith produced a magnificent reaction save to keep out a wickedly deflected drive from Ryan Colclough before Ajay Leitch-Smith rattled the crossbar in stoppage time.