The victory was tinged with sadness for the Crewe squad who wore special T-shirts as a show of support for grieving Alex team-mate Adam Dugdale. The 25-year-old defender's baby son died earlier this week, only a few days after his birth.
"I'm sure the players put that little bit extra in for him," said Crewe boss Steve Davis.
"We're a family. We're that sort of club. We rally and get behind people.
"Adam has not been into the club for a couple of weeks now.
"I phoned him on Saturday morning and he and Nicola were holding up as best as they could. I told him the players were behind him and they would try to do something for them."
Luke Murphy and Max Clayton scored the goals that secured a first-ever Football League Trophy success for the Alex.
The young pair are products of Crewe's renowned youth academy and, like Ashley Westwood and Nick Powell who left for Aston Villa and Manchester United respectively last summer, Murphy in particular is attracting interest from bigger clubs.
Southend headed back to Essex having still never won this competition, despite reaching three finals.
The game was only boss Phil Brown's third in charge since he took over from Paul Sturrock, who had initially been told he could return to lead out the side at Wembley before declining the offer.
But Brown is now focused on making up the six-point gap his side need to overcome to get into the League Two play-offs.
"I don't think it was the preparation that cost us," said Brown. "I've said to the players afterwards that we've got five massive league games.
"Results at the weekend went for us and that's the talk among the players. They now have two eyes on promotion.
"The glamour of the Wembley cup final has gone now and now we have to focus on Rochdale at Spotland on Wednesday night."
It is estimated that the win is worth over £1/4 million to the winners in gate recipts, TV money and merchandise. And despite defeat the cash will be a big boost for Southend who still have high hopes of finally getting the project for a new Stadium off the ground.
Planning permission was given in 2008 for a 22,000-capacity stadium at Fossetts Farm. Only last week the plans hit a new roadblock, as the Club and Sainsbury's reduced the amount of money they were willing to contribute to town-centre development, which was part of the deal with the local council.
As part of the deal the superstore will develop Southend's current Roots hall site for a superstore.