Valley came from behind to make a winning return to competitive action for the first time in eight weeks at the Old Northamptonians' Billing Road complex.
Having fallen behind just after the quarter of an hour mark, Dylan Parker levelled things up for Town on 42 minutes before Caine Elliott struck a late winner to give the visitors reward for a more assured second half performance.
Rugby's starting line-up showed two changes from the one that took the field at the end of October in the disappointing Vase exit at Dudley with David Kolodynski kicking-off his fifth spell at the club and Jamal Clarke back from injury.
Justin Marsden and Ryan Seal were the two players to miss out. Town made a sluggish start though, and they were made to pay for this when Ryan Archer was given too much room in the centre of the park before floating his shot wide of Sam Lomax into the net from twenty yards.
Kolodynski then had his side's first real effort of the game, but he could only blazed it over, with James Hancocks also way off target with a free-kick from a potentially dangerous position.
A strong appeal for a penalty was turned down after the ball appeared to strike a raised Chenecks' arm just inside the box, and a further shot from Kolodynski was this time comfortably gathered low down by home keeper Justin Greatorix.
The equaliser came after Charlie Evans did well when pressuring the hosts' back-line after a long upfield clearance and with the ball breaking for top scorer Parker to execute a crisp low finish past Greatorix with the half-time whistle looming.
Town's levels of performance noticeably improved after the restart and they pinned the home side in their own half for large periods of the new half, although without testing Greatorix to any great extent.
Parker almost capitalised on a quick free-kick from Danico Johnson and Liam Francis saw his shot at close quarters blocked away, with Evans also heading just over.
A half-volley from Parker was then deflected wide, as Rugby continued to push for a winner, Greatorix was finally called into action with a decent stop to another Evans header after neat interchange play between Kolodynski and Johnson.
At the other end, Northampton's threat was limited, although striker Ben Lewington did almost make Town's defence pay for some hesitancy midway through the half.
The goal finally came for Valley with just six minutes of normal time remaining, after Elliott had initially run strongly at the centre of the opposition defence, before then pouncing first on the loose ball to guide it over the line.
Substitute Seal had a good opportunity to double the margin as Town countered quickly late on, but he was denied by a covering tackle just as he shaped to shoot.
Hancocks also performed a well-time interception in stoppage time to ensure that the visitors held onto maximum points.
Line-up: Lomax; L Recci, L Thomas, Clarke, Francis; Hancocks, Elliott; Parker (Seal), Evans, Johnson; Kolodynski. Subs not used: C Thomas, J Thomas, Marsden, McNeil. Booked: None.
Northampton line-up: Greatorix, Muddiman, Davis, Watkin, J.Lewington, Ogden, Archer, Pardoe, Irwin, B.Lewington, Reeve. Subs: Deane, Sharpe, Sweeney, Mallard, Wiciak.