The Potters were dealt an early blow after only two minutes when both Ed de Goey and Gary McSheffrey challenged for a high ball on the right of the area but Stoke's first choice keeper came off worse, needing a stretcher to exit the pitch.
Coventry settled quickly and took full advantage of the Potters' inept performance as they were gifted shooting opportunities on several occasions. Michael Doyle was a whisker away on 28 minutes when his right-footed 20-yard strike flew over the bar.
However, against the run of play, Stoke won a free-kick just outside the box and after a Clive Clarke step over and John Halls' pass, promising youngster Kris Commons hammered his shot goalwards and into Scott Shearer's top right corner.
Graham Barrett almost replicated the goal seconds later but a fine Neil Cutler save prevented a Coventry equaliser.
Stoke had a lucky escape three minutes after the break when Stephen Warnock picked up a loose ball and hit a superb shot towards goal leaving Cutler grasping for thin air but, unfortunately for Coventry, his effort bounced back off the post.
Rousing support from the away fans sparked a Sky Blue resurgence but, despite heavy pressure from Julian Joachim and Calum Davenport, the Stoke centre-backs held out for the win.
Stoke manager Tony Pulis said: "It's been a very difficult week for us and probably one of the worst situations since I have been at this club concerning missing players.
"I am delighted that we have worked hard and got all three points as well as keeping a clean sheet."