Danny Hylton and Cameron Jerome's second half goals were enough to seal an eighth win in the last 12 Championship matches and ensure the Town are well in the promotion picture with less than a third of the seasono to go.
It was a memorable return to his former club for manager Nathan Jones, who made three changes to the side that beat West Brom on Saturday, with Reece Burke coming back into defence after missing out at the weekend, and Gabe Osho moving into midfield in place of Pelly-Ruddock Mpanzu.
James Bree was making his 100th appearance for the Hatters, whilst Danny Hylton made his second league start of the campaign and Harry Cornick returned in attack, supporting top scorer Elijah Adebayo.
Stoke had the game's first attempt on target, Tyrese Campbell's attempted curler easy for Jed Steer to gather in the Town goal with 18 minutes on the clock.
It was an uneventful opening half-an-hour, livened only by Allan Campbell's tussle with the Potters' Nick Powell that earned the Scot the first yellow card of the evening for a bout of wrestling just inside the Stoke half, with the Hatters looking solid at the back and Amari'i Bell especially on his game up against Campbell.
Referee John Busby wasn't as quick to spot a blatant foul by Campbell on the Town left-back by the touchline, but thankfully the Hatters backline saw off the threat of the resulting corner with Hylton and Cornick beginning to threaten at the other end, especially down the right flank.
It was down that side that Bree produced the cross for the Town's best opportunity of the half, a couple of minutes before the break, but Bell couldn't get anything on the end of it and the untroubled home keeper Joe Bursik saw the ball out.
Cornick was next into Busby's notepad in the 52nd minute for a tug on Powell as the ex-Manchester United man looked to break free and set Stoke on the attack.
A minute later came the Town's best moment as Adebayo set Cornick racing onto the ball down the right, and the forward went past his man to the byline and cut back looking for Campbell, but Joe Allen got there just ahead of him to clear behind.
Three minutes later, in a virtual carbon copy, the breakthrough came as Bree set Cornick racing away. He left Josh Tymon trailing in his wake once again and Hylton was there to steer in at the near post for his second goal of the season.
How the 581 travelling fans behind the goal loved it as their talisman hurdled the advertising boards to celebrate in front of them, Cornick pointing to the name on the back of the number nine's shirt in recognition of his contribution.
The lead should have been doubled in the 63rd minute as Cornick put Adebayo in the clear with a driving run and pass with the outside of his right boot, Bursik racing off his line and diving low to his left to prevent the top scorer adding to his 13-goal tally.
Campbell's attempted flick from Cornick's deflected shot might have caight Bursik out on 68 minutes, but Stoke survived as their fans started to show their frustration with the Hatters well on top and posing plenty of problems.
Adebayo came close again three minutes later when he latched onto Hylton's clearance, twisted and turned his way past the centre-half pairing of Liam Moore and Taylor Harwood-Bellis, before the Manchester City loanee got back to block his eventual shot.
The second goal did come in the 81st minute when Naismith crossed from the left, after a short corner, and Jerome - just six minutes after coming on for Cornick - produced an expert side-footed finish for his second goal in as many matches.
It was a nervy end for Jones' side after Lewis Baker had pulled a goal back in the second minute of added time but all in all, it was a dominant performance to ram the taunts of the home fans back down their throats as the Welshman masterminded the most perfect of away performances.