Colin Calderwood recorded his first victory in five matches as Northampton manager as his side fought out a hard 1-0 win.
Calderwood was appointed as the Cobblers boss in October following the sacking of Martin Wilkinson and a freak goal from Paul Trollope secured him his first win.
Calderwood said: "I am delighted we have got all three points and it was very important because we have got a break before our next league game.
"I would like to congratulate my players for their effort and endeavour that got them through some tough parts of the game today. I think everyone is understanding the way we want to play and their commitment was excellent." In an exciting first half, Southend were indebted to goalkeeper Darryl Flahavan for keeping the scores level with a superb double save.
Northampton winger Josh Low, a club-record summer signing from Oldham, ran at the United defence and played the ball to Martin Smith. His effort was blocked by Flahavan and Richard Walker looked likely to score but a follow up shot was smothered by the Southend goalkeeper.
United had numerous chances and Mark Gower broke free of the Town defence but could not beat Lee Harper from the edge of the penalty box.
Tes Bramble then put a header wide, Gower blasted over when well placed and Leon Constantine should have scored but his weak header was straight at Harper.
Northampton took the lead in the 60th minute when Trollope took a free kick near the right touchline following a Lewis Hunt foul on Martin Smith. Trollope crossed the ball into the penalty box but it missed everyone and bounced past Flahavan and into the net.
Southend had a great chance to equalise when they were awarded a 70th minute penalty. Jay Smith lobbed the ball towards Bramble but the striker was pulled to the floor by Chris Carruthers.
Smith took the spot kick but his effort was pushed out by Harper and the Town keeper did superbly to then stop Smith's follow up header.
This latest miss from the spot was the fifth penalty out of seven that United failed to convert this season.
Southend's day was summed up in injury time when Maher who had been booked in the first half was sent off when he received his second yellow card.
The Shrimpers were booed off the pitch and have now gone six home league games without a win.