Manager Chris Wilder praised a good performance, both 'individually and collectively' as his side gained a vital three points thanks to goals from Kouo-Doumbe and Dickenson.
New signing Zander Diamond slotted well into defence and the Cobblers will take plenty of heart ahead of a quick return to action for the second of three home games in the space of a week.
Southend were held to a goalless draw at York City on Saturday and have gone six games without a victory although they still occupy a play-off place.
"I just felt we didn't really do enough once again in the final third," said manager Phil Brown afterwards.
"We looked solid as a back four but York didn't really create too many chances. However, we are disappointed that we didn't put our best foot forward when we had the ball."