Jack Beckett's first half strike settled the Butlin Road battle between relegation rivals in Dynamo's favour.
The game as a whole was a poor quality affair, with Valley putting in a particularly disappointing performance - especially considering the enormity of the fixture.
Gary Moran made one change to the side that had battled to a victory at Northwich three days earlier, preferring to start with Chris Sterling in a wide role ahead of Robbie Parsons, and the early exchanges on the hard surface set the tone for the remainder of the game - with both teams struggling to get the ball down and execute any control as a result.
Ashley Hodgkinson did drag a decent chance wide for Loughborough though on six minutes, whilst Levi Rowley's wayward volley represented the hosts' only early effort, before the ball dropped kindly for Beckett just inside the box and he smashed it past Louis Connor.
Town's lacklustre opening period continued, and apart from a Mason Rowley volley which keeper Scott Wardley caught relatively comfortably and a Kyle Rowley downward header late in the half which bounced wide of the target, there was little sign of a equaliser from the home side.
The standard of the fayre on show did not really improve after the break, with the visitors happy to defend their lead and Rugby struggling to make any real impact on the game.
The hosts only threatening spell came around the hour mark, with a Levi Rowley shot deflecting over and Sterling's strike on the turn hitting the side netting.
Tevin Shakespeare also headed Ryan Quinn's looped cross over the bar from close range, before Dynamo's Roger Lee was sent off for a second bookable offence - with his manager Peter Ward also dispatched to the stands for protesting against the decision.
David Kolodynski almost helped in Quinn's shot from twenty yards, but it was the visitors that came closest to a goal when Hodgkinson somehow stabbed the ball wide from close range after Agyemang Ezekiel had flashed one across the face.
Mitchell Thomson also headed over the bar and despite a number of late free-kicks and corners which saw Connor join his outfield players in the box, it was the visitors who celebrated a vital three points on the final whistle.
Line-up: Connor; Print, Punter (Brathwaite), M Rowley, K Rowley (Fura); Thomson, Quinn, L Rowley (Parsons), Shakespeare, Sterling; Kolodynski. Subs used: Charles, Faulkner. Booked: Sterling.