With only five minutes remaining Dele Adebola pounced to end a personal six-game goal drought and earn Coventry all three points.
Stoke only had themselves to blame for their 22nd defeat of the season, Paul Gallagher and Darel Russell both spurned chances before Adebola struck.
With neither the threat of relegation or the promise of the play-offs, both sides struggled to break sweat in the opening 15 minutes and looked well worth their respective mid-table places.
Dave Brammer and Adam Rooney prompted excellent stops from Marton Fulop early on but the first real chance arrived in the 18th minute.
Evergreen midfield craftsman Don Hutchison's deft flick sent Gary McSheffrey through on goal and the striker's scoring reputation provoke a gasp from the home fans. But amazingly, the usually unforgiving Coventry sharpshooter let City off the hook with a tame effort when really he should have scored.
City's retort was swift and almost effective when six minutes later Mamady Sidibe was sent clean through, but with Fulop's goal gaping the Mali-born striker showed why he only has a return of five goals from 35 league starts by firing wide.
Stoke upped the tempo after the break and should have been reaping the rewards were it not for a distinct lack of confidence in front of goal.
Martin Paterson carved open the Coventry rearguard in the 50th minute, with a crafty reverse pass for the advancing Russell. The industrious midfielder fired wide though when all that was needed was to hit the target.
Gallagher wasted another good chance moments later, after chasing down Clint Hill's defensive punt. The striker ballooned over from just yards out.
The travelling contingent were forced to wait 20 minutes to see their side mount a meaningful attack in the second half. Kevin Thornton's jinking run opened up space on the edge of the Potters box, but the resulting shot lacked both power and precision.
But by now the visitors had the momentum and it wasn't long before they had a goal to go with it. Adebola finished off a fine approach with a powerful drive which Steve Simonsen could only flap at.