Goals from Anthony Straker and Freddy Eastwood secured the Shrimpers a comfortable win but the Cobblers were forced to play than an hour with 10 men after winger Chris Hackett was dismissed.
Northampton wasted a great chance to open the scoring after just eight minutes when former Shrimpers striker Roy O'Donovan saw his spot kick saved by Daniel Bentley who dived well to his left-hand side to parry the shot to safety.
To add to Northampton's frustration, Hackett was dismissed in the 22nd minute after being shown a second caution for a late challenge on Straker.
Southend then took the lead in the 38th minute when Straker scored his first goal for the club, heading home from close range after being struck by a long-range shot from Eastwood.
The Shrimpers then doubled their lead in the 68th minute when John White played in Eastwood who fired an angled 12 yard shot in to the bottom left hand corner of the net.