They did well the kids, but could only hold on to their precious lead 11 minutes, when the Hatters scored three times to win this reserve fixture played on a difficult pitch at Sharpenhoe Road, Barton Rovers home ground.
After a goalless first half of little interest first year scholar Duane O'Archie shot the Shrimpers in front five minutes after the break.
A Julian Okai corner found Duran Reynolds at the second attempt, he placed the ball into the path of O'Archie, who scored from a few yards out.
However, with several senior pros backing up their own youth players, on 71 minutes JJ O'Donnell equalised for the home side from close range.
After a triple substitution, Alex Lacey then gave Luton the lead only seven minutes later after a knock on from a set piece outside the area.
Recent semi-finalist on Sky show 'Football's Next Star, Hitcham Abdellah came on for the Shrimpers, but four minutes from the end Taiwo Atieno rifled the ball home to confirm victory at the expense of Ricky Duncan's hard working youngsters.
This was Luton reserves fifth win in their last six matches.
As for the Blues Two's, they finish off the season away to Stevenage Borough next Tuesday, May 4th, kick-off 19.00.
Southend United: Bentley, Ferdinand (Furlonge 70), Whittikar, Reynolds, Nesbitt, Milner (Smith 77), James-Lewis, Woodyard (Abdellah 70), Okai, Ekim, Ofon-Acheampong.
Luton Town: Gore, Denney, Caines, Lacey, Nelthorpe, Clarke, Poku, Wood, O'Donnell, Martell, Atieno.
Subs: Toomey, Harriott, James, Dasilva, Nathaniel.