The Sky Blues barely saw the ball in the opening five minutes, but with their first meaningful attack scored the opening goal.
Gary McAllister found space on the left to pick out Patrick Suffo in the box and the nippy Cameroonian skipped past Marcus Hall, lost his footing then recovered to poke the ball in from eight yards.
Then, after a speculative McAllister effort from 25 yards tested Ed de Goey in the Stoke goal, Graham Barrett added another on 11 minutes.
The Irish under-21 International beat ex-Coventry player John Eustace to a 50-50 ball then burst inside from the right flank, unleashing a vicious left-footed drive that left de Goey rooted to the spot.
Scott Shearer was then called into action twice to make good saves from Carl Asaba and Gifton Noel-Williams, however, a moment of madness from the young Coventry keeper brought Stoke right back into the game deep in first-half stoppage time.
Shearer ran out to meet the ball at the edge of the box but was beaten to it by Asaba, who lifted his half-volley superbly into the open goal.
However Coventry killed the game just before the hour mark. Steve Staunton lifted a free-kick deep into the Stoke box, Barrett knocked the ball back for Dele Adebola who turned well and slotted past de Goey.
Then substitute Andy Morrell popped up to seal a perfect afternoon for the Sky Blues with a clinical header from a Michael Doyle cross, before Wayne Thomas grabbed a 78th minute consolation for the visitors.