With Pelly-Ruddock Mpanzu and Henri Lansbury missing out due to knocks, while both Jordan Clark and Luke Berry remained unavailable too, it meant that Gabe Osho stepped up from defence to play alongside Allan Campbell.
The former Reading youngster has been used in that position before, which meant the more surprising decision was forward Danny Hylton dropping deeper to be just behind a front two of Elijah Adebayo and Harry Cornick.
With strict instructions to get around Wales international Joe Allen, the plan worked as the former Liverpool midfielder managed 60 touches and a passing accuracy of 71.4% on the night.
That was down from the 72 touches he managed in the 2-2 draw with Birmingham on Saturday, where his passing was 88.9%, while he also managed 84% in the 2-2 draw at Nottingham Forest too.
Hylton also got on the scoresheet himself too, breaking the deadlock early in the second half, before Cameron Jerome came off the bench to make it 2-0, as Lewis Baker's late strike was a consolation.
Jones said: Danny hasn’t played much, he was playing as a number 10, so it was a makeshift midfield.
"We had four midfield players out, Allan Campbell is the only midfield player there, we’ve got Gabe Osho who’s a centre half, Danny Hylton who’s a centre forward, playing against Joe Allen, Nick Powell and Lewis Baker, it’s phenomenal.
"For what we’ve done, for Danny to score, Cameron to then get a goal, a game-changer, it's a great night.
"Apart from Lewis Baker’s goal right at the end, it was pretty much perfection.”
On his different position in the side, Hylton himself said: “I found out yesterday I'm playing in a slightly deeper role, but it was a little bit more of a defensive responsibility, to stop Joe Allen getting on the ball and their midfielders getting on the ball, so a job to do there.
"But also I had a license to get forward and run in the box like I managed to do and try to create problems.”
When asked if he had ever played there before, or had much chance to prepare, Hylton continued: “Not too many times, but it’s not too dissimilar.
"It was more stop Joe Allen playing, he’s the one they try and build through, he gets on the ball and dictates play, so I had a bit of a job to do, a bit of responsibility to try and get to him when he had the ball.
"Then when we had the ball try and get in the box, we’ve got Eli (Elijah Adebayo) and Corny (Harry Cornic) who can do both, get in behind.
"Corny does a brilliant job, so my job was just to join in, try and make runs beyond them or try and support the play.
"I was a real tough pitch, it’s quite bouncy, quite lively, conditions were hard, so it was quite scrappy, but we’ve got three points.
"The boys did absolutely amazing, the boys put in a great shift, so I'm delighted to get three points.”
A scrappy first half had precious little in terms of genuine goalmouth action, but following the half time interval, Luton looked a different side, Harry Cornick in particular to the fore, causing a whole host of problems to the Potters with his direct running.
The attacker had a big role to play in Town’s first, delivering a low cross that Hylton met first time to clinically volley beyond Joe Bursik into the bottom corner.
ones said: “We had pace and energy in the side, that’s what we tried to recruit and that’s what we felt would win the game.
"Everyone can run, everyone’s fit, everyone’s durable, we've got no laboured players in our squad, and that shows the way we play and I’m proud of that.”
The goal also showed just why Jones was keen to use him the former Oxford striker in the position, knowing he had the predatory instincts to convert a chance should it come his way.
He said: “He's playing centre forward as a 10, so we knew we would be a threat if we could get enough balls in the box and when we did get that ball in the box.
"And let's be honest, we should have had more than two.”
Luton might well have added to their tally, Elijah Adebaypo missing a one-on-one and then being denied by a last ditch challenge as he looked to grab a 14th of the season.
Jones said “You can say he’s unlucky but if you finish those, if that’s 0-0 then they score late as a winner.
"But the way we carved them out and the energy we showed, we were constant.
"There was a lot of them going down with cramp late on, so it shows the levels we’re at and I’m super proud.”
Town did have the luxury of a second goal though with eight minutes left, former Potters forward Jerome, only just on for Cornick, converting an excellent corner routine that saw James Bree’s pass sent into the box first time by Kal Naismith.
Jones added: “That’s why we brought Alan Sheehan in.
"Since Alan has come in we’re as good as anyone in the league.
"We’ve been decent anyway with set-plays, but we’re as good as anyone now, top two or top three in terms of set-plays.
"We know we’re going to need so many different was to score a goal and we did that, so I'm just proud of the performance.”