Cameron Jerome struck on nine minutes after being fed by Joe Ledley and captain Darren Purse headed in a Jason Koumas cross two minutes later.
Paul Gallagher hit the post for Stoke after the break, but Cardiff continued to look the most dangerous with Jerome and Paul Parry going close.
Cardiff boss Dave Jones:
"We are building brick by brick - the foundations are coming along nicely but that is all we can say at the moment.
"This is a very tough division and there are many more tough tests to come.
"But this was a terrific team performance with everyone doing their jobs. I will just keep pushing the players on to do even better because that is the only way forward."
Stoke: Simonsen, Buxton, Hoefkens, Duberry, Broomes, Chadwick (Kolar 84), Mbuyi, Russell, Harper, Gallagher, Sidibe.
Subs Not Used: de Goey, Dyer, Halls, Henry.
Cardiff: Alexander, Weston, Purse, Loovens, Barker, Koumas, Ledley, Whitley, Cooper (Parry 79), Jerome, Ricketts (Lee 72).
Subs Not Used: Margetson, Cox, Ardley.
Booked: Ledley, Jerome.
Goals: Jerome 10, Purse 12, Jerome 43.
Ref: R Beeby (Northamptonshire).