Valley recorded a narrow victory over bottom side Chenecks in their final Butlin Road outing of the season.
Second half strikes from Justin Marsden and Caine Elliott ultimately secured Rugby victory, although the visitors did pull one back shortly after Elliott's goal to set up a tight finish.
Town made three changes to their starting line-up from the previous weekend's home victory over Wellingborough, with the suspended Harry Eden, the ill Adam Shaw and the late injury withdrawal Luke English replaced by Barry Fitzharris, Edwin Ahenkorah and Liam Francis.
The hosts started brightly enough, and they nearly took an early lead when Ahenkorah's effort from ten yards was blocked away by Northampton keeper Bradley Lashley after David Kolodynski had done well to put Lashley under pressure following a Madundo Semahimbo cross.
Kolodynski flicked a Marsden delivery wide of the target, before he did the same with a shot from distance, but generally it was a quiet opening half from Rugby.
The major talking point of the opening period came at the other end after Ash Bodycote had punched clear the ball into the path of Cam Mabbutt, who in turn struck the goal frame with his volley.
Confusion reigned thereafter, with James Hancocks hooking the ball away from the goalmouth, Chenecks striker Lewis Irwin unable to force home his rebound attempt and then the match referee appearing to indicate that a goal had been scored.
Fortunately after a consultation with his linesman, the referee reversed his decision and Valley escaped what would have been a clear injustice.
Town made a more potent start to the new half though, and took the lead just two minutes into it when Kolodynski's neat flick-on to Marsden in the penalty area saw the player-assistant manager fire one convincingly into the roof of the net.
The home side pushed on for a second, with Francis heading a Hancocks free-kick wide, and then Jamal Clarke doing the same to a further set-piece delivery from the same player.
Rugby were soon extending their advantage on 65 minutes though, when Elliott and Kolodynski combined well, with the latter unselfishly laying the ball into the path of the former for simple finish.
However Jonny Muddiman halved the arrears shortly after, with a similarly straightforward completion of an Emmanuel Annan pulled ball across the goal face.
Annan's deflected shot which drifted off-target was the closest the visitors came to an unlikely equaliser, whilst Barry Fitzharris twice went close to a third for Rugby before the game concluded.
Valley Line-up: Bodycote; Summerfield (English), Hancocks, Francis, Clarke (Recci); Fitzharris, Marsden, Elliott; Ahenkorah (Lock), Semahimbo, Kolodynski. Subs not used: None. Booked: Francis, Recci, Elliott.
Northampton line-up: Lashley, Muddiman, Davis, Ogden, Sargeant, Mabbutt, M.Smith, Falconer, Irwin, Ulker, Annan. Subs: Sharpe, Rowley, Kusi, T.Smith, Rait.