Giles Coke ended his 10-month spell on the sidelines with 56 minutes for the Cobblers reserves.
The second string put Southend to the sword 3-1 at Sixfields thanks to a brace from the impressive-looking Shaun Goodall and triallist Chris James' volley.
As well as Coke's first appearance in a claret shirt, there was another boost for first-team boss Stuart Gray, whose captain
Chris Doig played a full 90 minutes.
"Giles came through nearly an hour and it was good to see him back out on a football pitch," said reserves coach Ian Sampson.
"He was a little bit rusty but he'll be boosted from the playing time he got and I think his confidence will be sky high at the moment.
"When you've been out with a long-term injury all you want to do is play again so I am sure he was really looking forward to playing in this game and he did okay."