The Cobblers are now just two points above the drop zone and face a critical seven days with visits to fellow strugglers Brighton and Cheltenham.
But new Saddlers manager Chris Hutchings can afford to be more upbeat after goals from Stephen Hughes and substitute Jabo Ibehre, in injury time, gave the visitors three points they scarcely looked like achieving.
The opening goal arrived when Michael Ricketts threaded a defence-splitting pass to release Hughes, allowing the former Arsenal and Everton man to coolly slot passed Ron-Robert Zieler in the home goal, who was making his debut on a loan spell from Manchester United.
The second arrived in almost identical fashion, only this time it was Ibehre who slipped the home defence before beating Zieler.
Northampton boss Stuart Gray is refusing to push the panic button after four defeats on the trot, while the Saddlers are now unbeaten in four matches, although this was only their second success on the road in the League since September.
Gray said: "I would be more worried if we weren't creating chances and we had the better ones today, but you expect Mark Hughes, Andy Holt and Colin Larkin to hit the target with those sort of opportunities.'"
Hughes headed wide from close-range in the 13th minute after a long throw from Holt, while Holt headed over a Giles Coke cross in the 36th minute.
Before that, a Danny Jackman corner brought a header from Billy Clarke, which was saved by Clayton Ince before the rebound effort by Adebayo Akinfenwa was blocked on the line.
Substitute Larkin had chances to make an impact after replacing Clarke in the 68th minute, but headed an Akinfenwa cross wide when he should have done better.
Little was seen of Walsall as an attacking force until they struck with venom in the closing stages, although Anthony Gerrard had a second-half shot deflected on to the roof of the net.