Substitute Martin Paterson grabbed Stoke's opener with the Wednesday boss screaming for a foul on striker Marcus Tudgay as top-flight ref Alan Wiley refused to stop the game.
Sturrock,who slammed Premiership ref Steve Bennett for his handling of the game against Yorkshire rivals Leeds last month, was not a happy man.
The Potteries side, under pressure for most of the half, went ahead in the 34th minute, Paterson bursting through the Wednesday rearguard to draw Brad Jones off his line before slamming the ball into an empty net.
Chris Brunt had carved out an early opening passing inside to fit again striker Tudgay but his shot from 15 yards lacked power as Steve Simonsen scooped up his low strike.
Deon Burton linked with Tudgay minutes later as the Sheffield side almost grabbed the opener. Centre-back Clint Hill blundered as he moved in to clear but the Wednesday striker rushed his shot slamming his angled drive over the top.
Dominant Wednesday went close again Lloyd Sam threading the ball to full-back Frank Simek as he overlapped on the right before finishing from the edge of the box, the ball curling inches wide of the post.
The Sheffield side were caught on the break , Darel Russell given time and space to drill in a fierce shot pushed away by Brad Jones, midfielder Luke Chadwick steamed onto the loose ball but fired across the face of the goal, the ball drifting wide of the far post.
Stoke escaped in the 19th minute, dangerman Tudgay foiled by Simonsen and as the ex-Derby striker fired again the ball appeared to hit midfielder David Brammer but referee Alan Wiley turned away Wednesday's appeal for a penalty.
Wednesday almost broke the deadlock minutes later, centre back Madjid Bougherra stretching to meet Chris Brunt's precise corner as the Stoke keeper pulled off an eye-catching reflex save to tip his point-blank header over the bar before Paterson broke the deadlock.
Battling Wednesday were back on level terms on 40 minutes after Andy Griffin handled a deep cross and Brunt coolly finished with a stinging spot-kick.
Brunt almost snatched a second in the 58th minute with a spectacular strike from 30 yards, the ball flashing inches over the top.
The impressive Whelan was inches away before Tudgay squander the chance to snatch the winner with minutes to pulling his low shot wide from 15 yards.