Not much fun for the Shrimpers at Sixfield with Cobblers striker Steve Guinan nailing a hat-trick.
Southend gave a chance to Spurs youth Coskun Elgin, who started on the bench but the former London Youth Games 800m winner came on for the injured Osei Sankofa, a precaution after a clash of heads, after 38 minutes.
Northampton opened scoring with only three minutes on the clock after some indecision from Jean-Yves M'Voto, the Sunderland loanee carrying on from his disastorous half up at Hartlepool, gave Stephen O'Flynn the chance to find Guinan who passed the ball into the corner of the goal.
The Frenchman had earlier nearly headed into his own net and was taken off after only 12 minutes, a player of quality who is falling apart in front of our very eyes, there's a problem here, though his replacement Kane Ferdinand showed signs of quality.
Guinan grabbed his second just after the half hour mark with a header, and completed his treble 57 minutes, hitting home from close range.
O'Flynn finished the scoring for the Cobblers halfway through the second period when the always busy Michael Jacobs found the former Derry City striker who couldn't miss, and didn't.
Some good news for the Essex side was midfielder Stuart O'Keefe playing the whole of the first half in his bid to regain full match fitness from his hernia operation, and he felt fine after the game.
O'Keefe told www.southendunited.co.uk: "I felt really good and fit. As the first half went on it got a little bit stiff but the medical staff said that was to be expected. It's difficult training all week and I want to contribute to the team. I've not had the chance yet which is frustrating but I'll keep grafting."
Southend United: Bentley, Osifuwa, M'Voto (Ferdinand 12), Sankofa (Ekim 38), Nesbitt, Milner, James-Lewis, O'Keefe (Woodyard 46), Okai, Spencer, Crawford.
Subs not used: Chambers, Ofon-Acheampong.