Malky's defensive looking line up did their job to keep Stoke but it meant chances were at a premium at the other end.
A game that will not be regarded as a Premier League classic earned a point for City that saw them climb to 14th in the table.
Jordon Mutch's first half header and shots from Whittingham and John in the second half were the closest Cardiff came to a goal.
Stoke did put the ball in the net but it was ruled offside and the hosts were lucky to keep 10 men on the pitch after Charlie Adam twice had a go at Fraiser Campbell. Adam was already on a yellow when he pushed Campbell over in the box when City were waiting to take a free kick and he had raised arms in an incident near the touchline.
Now Cardiff face Crystal Palace in another game they can't afford to lose, but they must try to look for a win.
Adam looks away after shoving Campbell to the floor.
Match details
Stoke City Begovic; Cameron, Shawcross, Wilson, Pieters (Muniesa h-t); Nzonzi, Whelan (Ireland 65); Arnautovic; Adam, Assaidi; Crouch.
Subs: Sorensen, Pennant, Palacios, Jones, Walters
Cardiff City Marshall; Theophile-Catherine, Caulker, Turner, John; Cowie, Medel, Gunnarsson, Whittingham; Mutch; Campbell (Odemwingie 76).
Subs: Lewis, Connolly, Hudson, Cornelius, Bo-Kyung, Noone.
Referee: Michael Oliver (Northumberland)
Attendance: 25, 014