James McClean made the most of a Town defensive mix-up to give his side a 1-0 half-time lead over the Blues at half-time.
Boss Paul Lambert made one enforced change to his team with Jon Nolan replacing Flynn Downes, who had been suffering with illness before being replaced by Nolan on Wednesday.
Cole Skuse was back on the bench after recovering from illness with Trevoh Chalobah continuing in the deeper midfield role. Teddy Bishop started back-to-back games for the first time since November 2016.
Skipper Luke Chambers again missed out due to his foot injury with Bartosz Bialkowski wearing the armband.
Stoke, without a goal in four matches and an away win since October, made one change with James McClean replacing Benik Afobe as they moved to 4-5-1 rather than their more regular diamond.
Stand-in Blues skipper Bialkowski was the first keeper called into action, pawing away an awkward Tom Edwards cross from the right in the third minute.
But Town were beginning the game where they left off on Wednesday and on eight Judge tried a curling effort with the outside of his boot which looped not too far wide of Jack Butland’s right post without overly concerning the England keeper.
The two sets of fans subsequently paid tribute to probably England’s greatest ever keeper, ex-Stoke man Gordon Banks, who died earlier in the week.
Pennington did well to cut out a Tom Ince cross from the right in the 14th minute, then reacted quickest to clear after Myles Kenlock had dallied in the area.
Stoke were on top and a minute later McClean crossed from the left and the ball eventually fell to Joe Allen, who stabbed back to Ince, who rather fortunately for the Blues blazed well over.
Town subsequently had a decent spell and in the 20th minute Chalobah struck a low effort from the edge of the box through to Butland after a well-worked move down the right.
On 28 Stoke worked themselves a chance on the edge of the area but Ince’s shot deflected away from goal. Sam Vokes stuck out a foot but sent it wide and in any case was flagged offside.
The visitors largely continued to control the game and in the 34th minute - soon after McClean had been booked for a clumsy foul on James Bree - they went close to going in front.
Ince whipped over a cross from the right which Vokes headed over from eight yards when the Wales international will feel he should have done better.
Four minutes later, a low Ince cross from the right flashed across the Town six-yard box with no one adding the final touch and then just past the far post.
But it was far from all Stoke with the half having been an end to end affair and on 39 Bishop skipped into the area before sending a low ball across the box but too far in front of his team-mates.
On 41 Nolan almost found himself space to shoot as he broke into the area but was closed down, but a minute later the Potters took the lead after a disastrous mix-up in the Town defence.
Knudsen got to a ball played into the Town box from the left ahead of McClean, with Pennington also in attendance, and the Dane headed back towards goal. However, Bialkowski had come off his line and the Irish international was able to turn into an empty net from a matter of inches.
Judge shot over and then cut in from the left and struck an effort which Butland claimed to his left as the Blues sought to get back on terms immediately.
There was applause for the Blues as they left the field at the break having been a touch unfortunate to be behind given the nature of the game.
Stoke, however, with Peter Etobo impressive in their midfield, had shaded the half having created the better opportunities with Vokes missing the best of the game’s earlier chances.
The Blues had put together some neat moves but as so often of late with the final ball or shot going astray and Butland hadn’t been significantly stretched. However, on their first-half showing they’re by no means out of the game, as long as they can get themselves on terms sooner rather than later once the second period gets under way.
Town: Bialkowski (c), Bree, Pennington, Knudsen, Kenlock, Chalobah, Nolan, Bishop, Judge, Quaner, Keane. Subs: Gerken, Edwards, Skuse, Jackson, Nsiala, Dozzell, Dawkins.
Stoke City: Butland Edwards, Batth (c), Martins Indi, Clucas, Woods; Allen, Etebo, Ince, McClean, Vokes. Subs: Federici, Bauer, Williams, Shawcross, Adam, Bojan, Afobe. Referee: Scott Duncan (Northumberland).