The volatile atmosphere didn't face the visitors and they stamp their authority on the game straight away.
Ian Moore's header in the sixth minute acted as a warning shot as it looped over Steve Simonsen's crossbar but Michael Duff went closer two minutes later.
His controlled header wrong footed Wayne Thomas allowing the midfielder to shoot from 15 yards, but his low shot was dragged wide of the goalkeeper's right post.
Stoke replied and to better effect when after Brian Jensen was pressured, Darel Russell's header was looped on by Gifton Noel-Williams and bounced over off the crossbar.
An intricate free-kick in the 58th minute by Noel-Williams gave Russell the chance to shoot, but he failed to hit the target, fluffing it wide from 18 yards.
Tony Pulis attempts to freshen up his attacking options with the addition of Chris Greenacre and Lewis Neal, but they made no impact leaving the home side scratching their heads.
City's best chance of the game came in the 65th minute when Ade Akinbiyi's deflected shot fell to Clive Clarke, but the captain's follow-up was tame, rolling out for a corner.
After soaking up several spells of pressure, Burnley countered in the 79th minute to good effect.
A left side corner by Tony Grant caused mayhem in the Stoke box and when the defence failed into clear, Gary Cahill was on hand to poke home from close range.
The Potters offered up no reply after that, leaving their former employee the victor.