Town slipped to a second successive league defeat after putting in a below-par performance at the Dog & Duck Stadium.
Wellingborough's Lloyd Buckby scored the only goal of the game on the hour mark to deservedly earn his side the victory against a Valley line-up lacking any level of creativity or cohesion on the day.
David Kolodynski, Melu Mpande and Max Johnson were back in the starting eleven from the reverse at Coventry five days earlier, but Rugby nearly found themselves a goal down in the opening seconds when Jake Newman got in behind the away defence - only to see Ben Newey keep out his well-struck volley.
Newey also did well to deal with a follow-up attempt, and later comfortably gathered ex-Valley man Robbie Parsons's shot, as the good start by the hosts continued.
Rugby were struggling to gain any foothold on the game, although Kolodynski did break free from his marker at one point to then round home keeper Josh McAdoo, but his final cross into the goalmouth was easily headed away by a covering defender.
Wellingborough continued to worry Town on occasion at the other end - most often from set-pieces, with Buckby having a shot blocked in the box after he had pounced on a corner. Max Johnson's free-kick from a wide position was easily taken by McAdoo in a rare attacking highlight for Valley, with Dylan Parker and Justin Marsden also putting their efforts way off-target.
The hosts then missed the chance to open the scoring, when Harry Chipchase screwed his penalty horribly wide after Josh Thomas had lunged late into the back of Parsons in the area.
Rhys Kelly also spurned a great opportunity for the game's opener in the closing minutes of the opening period, when he fired wide of Newey's frame after Rugby again failed to deal effectively with another corner.
Town's best chance of the game came shortly after the restart when Loyiso Recci's header to Johnson's corner was blocked on the goal-line, but generally there was little sign of an improvement from the visitors.
The goal came after Louie Barratt eased past Mpande down the hosts' right wing and he clipped a cross onto the head of Buckby to nod home from close range.
Town boss Carl Adams made an immediate triple substitution at this point with Danico Johnson, new signing Edwin Ahenkorah and Jordan Hawyard summoned from the bench to try and provide a positive impetus.
There was a marginal improvement to Valley's play from this point, but they still lacked any real incision in the final third and rarely troubled McAdoo in the home goal.
Ahenkorah could only help Hayward's powerfully driven cross wide, Kolodynski lifted his shot into the keeper's hands from an angled position and Danico Johnson put his effort from a tight angle onto the roof of the net, with Hawyard wasting the visitors' final chance of an equaliser with a wild lash at the ball to send it out of the ground.
Line-up: Newey; Josh Thomas, Mpande (Hayward), Loyiso Recci, Elliott; Hancocks, Max Johnson, Fitzharris; Marsden (Danico Johnson), Kolodynski, Parker (Ahenkorah). Subs not used: Francis, Bennett. Booked: Max Johnson, Hancocks, Fitzharris.
Wellingborough line-up: McAdoo, Anderson, Osoimoejiokhian, McBride, O'Connor, Kelly, Barratt, Chipchase, Newman, Buckby, Parsons. Subs: Uche, Lamb, Dench.