Town fell to their third away defeat of the UCL campaign last Saturday, conceding a goal in each half at Billing Road.
A missed Fazel Koriya spot-kick meant they missed out on a chance to level things up before the interval having fallen behind as part of another lacklustre opening 45 minute display from Carl Adams's men.
Further squandered opportunities after the restart let the hosts in to wrap things up with a second strike with twenty minutes remaining.
Adams made just one change from the previous weekend's narrow victory at Cogenhoe, with Danico Johnson restored after a one match suspension in place of Lewis Rankin.
The first chance of the game did fall to Valley though, when Charlie Evans beat a couple of players to force himself into the area before putting a weak shot straight at Chenecks keeper Jack Taylor.
The home side took the lead not long after, with Tyrell Bernard heading home Brandon Williams's deep cross from the right which Town's keeper Matt Hill failed to claim.
A carbon copy move and delivery then almost saw Northampton double their advantage, but this time Bernard guided the ball into the side netting.
For Rugby, Simeon Tulloch put one way over the bar after weaving into the box, before they were handed that potential lifeline from the spot when Evans was halted illegally after he had ran onto Loyiso Recci's long ball forward.
However Taylor was across well to keep out Koriya's penalty, and the hosts held onto their deserved lead at the break.
Town started the new period brightly though, and Harry Holloway was soon seeing his shot deflect just wide after Taylor had initially smothered out Johnson.
From the ensuing corner by Koriya, Recci lifted one over from close range and the defender also went close from a further set-play when he headed substitute Rankin's corner wide of the target.
The miss of the game came after Johnson had streaked past his man to cut back to Rankin, who somehow failed to score from a yard or so out, with the loose ball falling to Evans - whose powerful strike was blocked en route to goal by a defender.
Johnson also had an effort blocked after another Rankin corner, before poor defending by Josh Steele let in Chenecks for their second - with Williams's deflected shot beating Hill after Bernard's initial strike had come back off the post.
Koriya's near post header was straight at Taylor, as Rugby looked to salvage something from the game, whilst consecutive free-kicks from Rankin were both off-target before an afternoon to forget for Valley came to an end.
Line-up: Hill; Rosser, Recci, Steele; Tulloch, Kavanagh, Blythe, Holloway (Rankin), Evans; Johnson, Koriya. Subs not used: Blake, Marsden, Perkins, Adams. Booked: Johnson
Chenecks line-up: Taylor, Davis, Garlick, Watkin, Lewington, Nagy, Ogden, Bernard, Frost, Williams, Oliver. Subs: Green, Tolworthy, Foster, Irwin, Sharpe.