John-Joe O’Toole’s early opener was cancelled out by Jason Demetriou’s penalty but Matt Grimes scored from the spot before Alex Revell’s late third lifted the Cobblers to within two points of safety as Southend suffered a sixth league defeat in seven.
The first half was short on quality and that was epitomised by Northampton’s opener in the 19th minute.
After Mark Oxley beat away Ash Taylor’s header, Harry Kyprianou’s attempted clearance cannoned off Matt Crooks and fell for O’Toole to guide the ball into the bottom corner.
The lead lasted just seven minutes, however, as Taylor collided with Stephen McLaughlin in the box and Demetriou slotted home the resulting spot-kick.
But the visitors were behind again early in the second half when Chris Long was fouled by Kyprianou for a penalty which was dispatched confidently by Grimes.
Cobblers debutant Hildeberto Pereira hit the crossbar moments after coming on before he set up the game-clinching third, slipping in Revell who found the bottom corner.