Former Alex loan striker Lee Barnard did the damage on his return to South Cheshire with an early and late finish proving decisive.
But Crewe were their own worst enemies as well as Gary Roberts and Kenny Lunt both missed from the penalty spot.
The game was only 70 seconds old when Barnard capitalised on some sloppy defending to fire a low finish past Ben Williams.
While Crewe rallied with Dean Morgan heading Joe Anyinsah's cross at Darryl Flahavan, Southend strengthened their grip on the game in the 18th minute.
Alan McCormack slipped James Walker in behind the last man and the youngster, who is on loan from Charlton, finished off, although keeper Williams did manage to get a glove to almost keep out the effort.
Peter Clarke's badly-timed challenged on Nicky Maynard presented Crewe with a 33rd minute penalty. But Roberts, who had scored two out of two from the spot previously, saw his effort beaten out by a brilliant save by Flahavan.
Crewe rallied after the break and, although Southend still held all the aces, a mistimed tackle from Simon Francis left Anyinsah sprawling in the box. Lunt took the responsibility this time, but Flahavan again was agile and kept out the 73rd minute kick.
Undeterred Crewe responded within a minute when Maynard headed home a Lunt free-kick.
Barnard wasn't finished and when he ran on to McCormack's throughball with ten minutes left he tucked away his finish into the far corner.
"We had a very poor start and I accept full responsibility and quite clearly I haven't done my job properly to prepare the players," said Holland.
Southend manager Steve Tilson added: "We made hard work of it in the second half and got a bit sloppy at times, but the finishes from Barny and James Walker were top quality."