Once the Potters had taken the lead midway through the first half the Bluebirds barely looked like getting back on terms.
Warren Feeney and Steve MacLean led the line in the absence of the injured Robbie Fowler and it was Stoke keeper Steve Simonsen who had to make the first save when he palmed away a Trevor Sinclair cross in the fourth minute.
The visitors took the lead in the 27th minute following a disputed corner. Liam Lawrence whipped the cross over and it was deflected on to the debut-making Ryan Shawcross who slammed the ball into the corner of the net from close range.
Joe Ledley and MacLean had shots blocked as the Bluebirds tried to get back on to level terms but the high balls delivered into the box were easily cut out by the Stoke defenders.
The visitors should have doubled their lead three minutes after the break but Ricardo Fuller was tackled by Roger Johnson just as he was lining up a shot with only Ross Turnbull to beat.
The Bluebirds were finding it hard to penetrate the Stoke rearguard and, with no striker on the bench, there seemed no way back. Paul Parry and Peter Whittingham were brought on in an effort to push the game Cardiff's way.
Whittingham replaced the injured Stephen McPhail and slotted into a central midfield position but Turnbull was the busier of the keepers, turning one shot from Mamady Sidibe round the post when the former Swansea striker should have extended his side's lead.
Cardiff were thrown a lifeline in the 87th minute when MacLean was pulled back in the penalty area but his weak spot-kick was saved by Simonsen who then palmed away the rebound.