The Welsh side had former Town striker James Collins in their attack, but it was goals from Rubin Colwill and captain Sean Morrison either side of a Jordan Clark equaliser that saw them run out 2-1 winners at a freezing cold, windswept Kenny.
Simon Sluga was back between the sticks after serving his isolation period, while Amari'i Bell returned to defence at left-back.
Glen Rea was named in the side for the first time since the away defeat against Preston North End in October, alongside Pelly-Ruddock Mpanzu and Jordan Clark in midfield - the latter of whom came off the bench in the midweek draw at Nottingham Forest.
Harry Cornick was the fifth change, partnering Elijah Adebayo up front as the Hatters go in search of a first win in four matches.
The visitors had the lead on ten minutes when Perry Ng crossed deep from the right, and Rubin Colwill was unmarked at the far post to head past Sluga, who clawed the ball away but goal-line technology had ruled the goal should stand.
The Hatters were struggling to get in the game, and Ng was the next to have a go at Sluga's goal, but his 35-yarder was well off target.
It took half-an-hour for the Town to get some decent possession in the Cardiff third, Clark and James Bree sending crosses in from the right that were well dealt with by City keeper Alex Smithies and his defence.
Adebayo looked to be in the clear on 38 minutes, only for City captain Sean Morrison to pull him down. Referee Oliver Langford showed a yellow card, deeming that Mark McGuinness was on the cover, and Kal Naismith's 20-yard free-kick proved too high.
Cardiff started the second half in similar vein to the first. McGuinness heading over, Colwill drawing a save out of Sluga and Marlon Pack firing over the bar from distance within the first six minutes, before Mpanzu drove one narrowly over Smithies' bar in the 52nd minute.
Adebayo found space on the right a minute later and crossed low for Cornick, who was denied by the Bluebirds' keeper at his near post.
Jones made his first change three minutes before the hour mark, bringing on Fred Onyedinma in place of Bell at left wing-back.
The Hatters' best chance of the game to that point arrived in the 62nd minute, as Naismith whipped in a cross from the left that Lockyer met with a glancing header that again was too high.
The breakthrough finally came when Naismith swung another one in from the left, Adebayo controlled and intelligently cut a perfect ball back for Clark to sidefoot calmly into the bottom corner of the Cardiff net.
Jones introduced Danny Hylton for Cornick a minute later, but it was Cardiff who retook the lead in thr 76th minute when Morrison met Ryan Giles' cross from the left with a firm header past Sluga from close range.
The Hatters, who had been by far the better side in the second half, went straight up the other end and created another opening for Clark, Naismith again sending a low ball in from the left but the midfielder couldn't direct his shot on target.
Bree shot high over the bar and into the top of the Kenilworth Road end with five minutes left, then Sluga had to race off his line and slide tackle Isaak Davies as the Cardiff sub looked to latch onto a through pass from Moore.
Goals:
Town: Clark 64
Cardiff: Colwill 10, Morrison 77
Att: 9,987 (1,032 away)
