Goals by leading scorer Andy Kirk and a late winner from substitute Ryan Gilligan meant that Damian Spencer's second-half header counted for little and left caretaker manager Keith Downing cursing his luck as Cheltenham have now gone seven matches without a win.
Kirk set the ball rolling in the 22nd minute when he turned sharply in the box to fire a shot past Shane Higgs and Northampton should have cashed in on early dominance to make the game safe by half-time.
Kirk's strike partner, Poul Hubertz, was returning to the side after suspension and he was denied when Higgs rushed from his goal to bravely save, while only a tremendous last-ditch tackle by Dave Bird in the 32nd minute denied Andy Holt the chance of making it 2-0.
Cheltenham rallied as the interval approached and Jennison Myrie-Williams, on loan from Bristol City, tested Mark Bunn from the edge of the box, while a Spencer header, following a cross from Paul Connor, dropped only inches wide with Bunn watching helplessly.
But Spencer had better luck five minutes after the re-start when he timed a late run into the box to perfection to meet a superb deep cross from former Aston Villa stalwart Alan Wright, Spencer heading into the top corner.
Cheltenham could even have gone in front when Spencer teed up John Finnigan in front of goal, only for the midfielder to miskick, before seconds later heading wide at the near post.
Northampton almost regained the lead with a left-foot blast from Bradley Johnson which screamed into the sidenetting, while Hubertz was inches away from scoring with 20 minutes left when he placed a careful header wide of the target from a Jason Crowe centre.
If the home side were starting to lose faith, their frustration was ended by substitute Gilligan's sweetly struck half-volley from the edge of the box in the 80th minute after Cheltenham could only half clear a long throw from Holt.