The Cobblers were beaten for a fifth successive game and will begin 2015 just two points off the Sky Bet League Two relegation places.
Marc Richards’ 12th goal of the campaign was not enough to take anything from their final game of the year at Prenton Park, where Tranmere Rovers ran out 2-1 winners.
Goals from Kayode Odejayi and substitute Jake Kirby secured that outcome and mean Rovers are now just two points behind Northampton.
The win lifted Rovers out of the bottom two, where they were replaced by Dagenham & Redbridge who have an inferior goal difference.
Chris Wilder shuffled his pack for the game, making five changes and switching to a five-man midfield to line up against Tranmere’s diamond in that area of the pitch.
Their early attacking play revolved around getting the ball into lone striker Marc Richards quickly and from deep areas, with mixed results.
Any semblance of attacking flow was disrupted by yet another pair of injury setbacks on the half-hour mark with Zander Diamond (hamstring) and Gregor Robertson (ribs) both replaced, by Kelvin Langmead and Evan Horwood.
Moments later the visitors were behind, Janoi Donacien collecting a throw-in high on the right wing and picking out Odejayi at the front post for a volleyed finish.
The striker took the chance well but the marking - as it has been in many of the recent defeats - was questionable to say the least.
After the goal, Northampton had a lot of the play but it did not look like they would breach the back line until Richards scored.
That he did owed a lot to Joel Byrom, who was gifted the ball by the Tranmere defence but still took an excellent first touch before threading in Richards to thrash home a deserved equaliser.
Rovers had a couple of half-chances with distance shots early in the second half but the better play was from the Cobblers, who forced a good save from Owain Fon Williams through Byrom’s firm effort.
But Tranmere retook the lead on 63 minutes when Jake Kirby curled a shot past Duke’s left hand with his second touch after coming on as a substitute.
Marcus Holness breathed a sigh of relief when his skimmed header from a Danny Alfei cross beat his own goalkeeper but a team-mate was on hand to clear off the line amid appeals for a goal.
Alfei himself was on the receiving end of a clever Evan Horwood cross in the final five minutes of the game but while he timed his run to perfection, his sidefooted finish was high into the stand.
Tranmere Rovers: Fon Williams; Donacien, Thompson, Holness, Holmes; Power, Jennings, Shuker, Laird; Odejayi, Fenlon
Subs: Stockton (for Odejayi 42), Kirby (for Jennings 62), Madjo (for Fenelon 90)
Not used: Brezovan, Baggie, Rowe, Jahraldo-Martin
Northampton Town: Duke; Alfei, Collins, Diamond, Robertson; Hackett, Byrom, O’Toole, Murdoch, Mohamed; Richards
Subs: Langmead (for Diamond 32), Horwood (for Robertson 33), Sinclair (for Mohamed 67)
Not used: Carter, Tozer, Snedker, D’Ath
Cobblers fans: 350