Jay Emmanuel-Thomas' first goal as a Town player wasn't enough as Northampton came from behind to win 2-1 at Portman Road and knock the Blues out of the Carling Cup.
Paul Jewell used the tie to give a number of fringe players a run-out, with the likes of Luke Hyam, Jaime Peters and Jack Ainsley being given a chance to impress the Town boss.
The game started at a frantic pace with both sides pushing men forward in search of a breakthrough.
The deadlock was broken after just 11 minutes with Emmanuel-Thomas scoring a stunning goal from distance which caught Northampton 'keeper Sam Walker off-guard and flew into the top corner.
Emmanuel-Thomas was looking sharp, playing just off the front two, and after some good build play from Town the summer signing fired in a shot at the second attempt that fizzed just wide of the post.
Almost immediately the visitors nearly drew level, after a rare attack saw striker Jake Robinson in space in the box but he rushed his shot and fired high over the bar.
More good work from Emmanuel-Thomas saw him charge the length of the field before switching the play with a fine pass to Jason Scotland, but the striker's fierce drive was well saved by Walker.
Despite Northampton looking dangerous on the break, Town were beginning to control the play and more good build up work almost delivered another goal.
Andy Drury found space on the right after being fed by Peters, and he produced a teasing centre that skipper for the night Colin Healy headed over from six yards.
And Town were made to pay for that miss just minutes later as Ben Tozer levelled the scoring with a cool finish at the second time of asking, after playing a neat one-two with Robinson.
Grant Leadbitter emerged for the second half to replace Hyam and the midfielder was straight into the thick of the action, firing a shot from distance just over the bar with Walker well beat.
However it was Northampton who were next on the score sheet. Good work on the left hand-side by Michael Jacobs saw him whip a low cross in to the Town box which wasn't dealt with by Tommy Smith and allowed Paul Turnbull to ghost in at the back post to tap home.
The Cobblers almost extended their lead just before the hour mark, when a Jacobs free-kick to the back post was met by the head of Tozer but he couldn't keep his effort on target and the ball flew over Lee-Barrett's bar.
Again it was the visitors who were looking the more threatening in front of goal, and it took a good stop with his legs by Lee-Barrett to deny Bas Savage adding a third for Northampton.
Town hit back looking for an equaliser, and came close to levelling with 12 minutes to go. Aaron Cresswell whipped in a cross but Emmanuel-Thomas couldn't find the target with his header.
Lee Martin then tried his luck just a minute later, with the winger cutting inside before unleashing an effort from distance that went narrowly wide of Walker's post.
The Northampton 'keeper then came to the visitors rescue with just five minutes to go as he kept out a well struck drive from Emmanuel-Thomas but the Cobblers held firm to repeat their giantkilling heroics of last season.
Town: Lee-Barrett, Peters, Cresswell, Ainsley, Smith, Hyam (Leadbitter 46), Drury (Martin 60), Healy, Emmanuel-Thomas, Scotland, Ellington. Subs not used: Cropper, O'Connor, Murray, Whight, Lawrence.
Northampton: Walker, Corker, Tozer, Webster, Davies, Robinson (Young 78), Savage (Langmead 90), Turnbull, Ofori-Twumasi, Jacobs (McKoy 90), Westwood. Subs not used: Hall, Thornton, Purcell, Akinfenwa.