Richard Money's side have not been beaten on the road since September 1st and they ground out another success with goals from Mark Bradley and substitute Ishmel Demontagnac.
It is a different story for Northampton boss Stuart Gray whose side have now lost their last four League matches without scoring a goal, and Gray stressed he would be looking for greater urgency when team changes seem inevitable in the FA Cup.
A lifeless first half was only lit up in the closing minutes, firstly with a brave save from Mark Bunn at the feet of much-travelled striker Michael Ricketts. Bunn also earned his corn in the 44th minute when he pushed away Darren Wrack's stinging 30-yard drive.
But the home team's relief was short-lived as Walsall grabbed the lead courtesy of Bradley, who capped an excellent week after scoring for the Welsh Under-21 side in a victory over France in midweek.
He latched onto a throughball from Ricketts and, although his first shot was saved by Bunn, he was able to coolly place the rebound into the net.
Bradley Johnson went close to equalising when he cut in from the right before firing a 20-yarder which whistled just wide while Gray showed his frustration by making a triple substitution in the 57th minute.
It almost had the desired effect when Poul Hubertz went close with a glancing header from Colin Larkin's cross, while Northampton were convinced they had equalised 12 minutes from time only for the match officials to rule that Guy Branston's header from Daniel Jones' corner had not crossed the line.
After Mark Hughes had headed wide for the hosts, Walsall bagged their killer second four minutes from time when Bradley broke down the right and squared a perfect cross for substitute Demontagnac to fire post Bunn.