Cheltenham fell to their fourth consecutive league defeat and the early season promise shown by the injury-hit Robins has now faded fast.
In truth, this was a poor quality game and Cheltenham wasted a golden chance to take something from it when Grant McCann blasted a second-half penalty over the crossbar with the score at 1-1.
The first half was a drab affair with both sides trying to play a passing game but going nowhere in a hurry.
Cheltenham's Brian Wilson forced a good save from Northampton goalkeeper Mark Bunn in the second minute with an opportunist shot from the edge of the box, while at the other end Andy Kirk saw his shot parried by Scott Brown after a neat exchange of passes with Pedj Bojic.
Cheltenham went remarkably close to scoring in the 14th minute when a clever reverse pass from JJ Melligan found Steve Guinan in the box. His low drive at an angle appeared goalbound until it hit his own player Kayode Odejayi and bounced out for Bunn to collect.
Northampton's Eoin Jess shaved the outside of a post shortly before the break but once again Bunn was tested at the start of the second half when he got down to block a Brian Wilson volley.
The second half proved marginally better than the first for the spectators and the first goal arrived with 67 minutes played.
Cheltenham defender Gavin Caines brought down Scott McGleish on the edge of the box and Jess's free-kick was deflected in by Kirk.
McCann made an awful mess of his penalty four minutes later having been brought down in the box himself by Sean Dyche.
And the Cobblers sealed the points seven minutes from time when defender Jason Crowe ran on to a pass from substitute Mitchell Cole and was tripped by Melligan.
McGleish thumped the spot-kick in off the goalkeeper's legs.