Shane Cansdell-Sherriff put Town in front on 55 minutes and Marvin Morgan doubled their lead soon after to seal victory.
Wolves should have take the lead early on but Alex Hemmings fired wide when one-on-one with the hosts' keeper Ben Smith.
Chances fell at both ends before Cansdell-Sherriff met Jon Taylor's cross at the near post with a header past Dorus De Vries.
De Vries was then forced into action to deny from Terry Gornell and Mark Wright but he could do nothing when Morgan finished off a fine passing move.
Stoke City also fell to defeat to lower league opposition, the Potters going down 1-0 at Brentford.
Charlie MacDonald's second-half header for the League One side was the only goal of the game at Griffin Park as new Stoke signing Jonathan Woodgate watched from the stands.