Just as in the reverse fixture in August, Jesse Friend's first half goal settled a dour affair at The Dovecote as Valley's poor form continued into the New Year.
The game was a once more a largely unforgettable spectacle played in high winds and at times driving rain on a difficult pitch, but it was the hosts who adapted better and enjoyed the lion's share of the few chances that were created during the 90 minutes.
Bleu McNeil, Callum Griffin and Stan Anaebonam were back into the Town starting eleven for the game, with Rivel Mardenborough, Teddy Rowe and Jack Concannon all relegated to the bench to make way for them.
Sam Tye's header to a deep Will Harris cross failed to trouble Shepshed keeper Mitchell Leivers early on, but the first real opportunity of the game came when Leivers's counterpart Marcus Bald hesitated when dealing with a hopeful ball behind the Town defence, but Geoffrey Lundoloki was across to clear away the danger.
Tyrell Hamilton almost latched onto one at the other end, and then Dynamo winger Jude Collins had a shot blocked, before the hosts missed out on two gilt-edged opportunities to take the lead from Declan Peart's long-throw - with Friend's header pushed onto the bar by Bald and Niall Prenderville also striking the horizontal with a follow-up header.
Shepshed did break the deadlock shortly after though, with Bald spilling Collins's fairly innocuous-looking shot at the feet of Friend, and the striker duly bundled the ball in from close range.
Bald then partially redeemed himself with a strong one-handed save from Aaron Korpal's well-struck rising effort, before Leivens gathered Lundoloki's deflected cross at his near post at the second attempt in a rare Valley attacking play.
Bald again did well with a full-length diving stop to push Collins's strike from distance behind for a corner, and Peart's headed one straight into Bald's arms, with another Lundoloki cross drifting too high for its target in the final minutes of the first-half.
The second period generated even fewer goalscoring opportunities than the first had, although Rugby did finally register their first shot of significance on 55 minutes when Anaebonam cut back in from the byline to fire one high and wide of the target.
Prenderville then headed wide Peart's cross to the back-post, before Caine Elliott shot way over and Collins did likewise for the home side.
The best chance of the second-half saw Bald down well to parry Jowan Partridge's curled strike - with Friend this time unable to successfully force home his rebound attempt, and despite some late Rugby pressure, the hosts were steadfast in dealing with this and secured the double for ex-Town assistant Gary Drake against his previous club.
Valley
Line-up: Bald; McNeil, Harris (Mardenborough 62'), Thomas; Kabeya, Lundolok, Griffin (Oben 77'), Elliott, Tye (Rowe 77'); Anaebonam (Concannon 77'), Hamilton (Charles 77'). Subs not used: None. Booked: Thomas, Lundoloki.