The Hatters were sent to the foot of the table in midweek after a 10-point deduction for entering administration.
But the Bedfordshire club put their off-field woes behind them as Calvin Andrew struck 16 minutes from time to seal the three points.
The hosts almost got off to a flying start but were denied by a superb save from visiting goalkeeper Steve Collis in the 13th minute.
Dave Edwards, fresh from his exploits for Wales in Germany in midweek, looked to have looped in a 12-yard header after Richard Jackson's curling cross from the left, but Collis extended an arm to tip the ball on to the crossbar and away.
After that escape, the Shrimpers then spurned a great opportunity to take the lead themselves four minutes later as Matt Harrold missed from the spot.
Jackson was the guilty party, tripping Gary Hooper after mis-controlling the ball in the area, but the Luton defender's blushes were spared by keeper Dean Brill, who dived to his right to save Harrold's low strike.
Brill came to the rescue again in the 21st minute when he tipped Garry Richards' thumping header over the bar after Kevin Maher's corner.
Marc Wilson, making his home debut for Town, sent a 16-yard header at Collis from Matthew Spring's driven free-kick seven minutes later as the hosts responded.
But Luton's frailties at the back were exposed again a minute later as left-back Adam Barrett ghosted in on to a Steve Hammell free-kick only to nod just past the post from eight yards.
The Hatters were dealt a blow two minutes before the break as Bolton loanee Jaroslaw Fojut was replaced by another loan signing Anthony Grant.
As the game degenerated into a scrappy midfield battle, chances were few and far between for either side.
A rare moment of attacking invention in the 55th minute saw Hooper wriggle past two tackles and tee up Nick Bailey to fire over left-footed from 20 yards.
Luton finally picked up the pace and were rewarded in the 74th minute when Spring's cross found Andrew at the far post and the striker couldn't miss from two yards out.
Andrew should have made it two in the 81st minute when he drew Collis but fired wide.
The miss gave Southend hope and the visitors almost salvaged a draw two minutes from time when Bailey screwed his shot badly wide when well placed 14 yards from goal.