Early signs pointed to a drastic improvement in the Stoke side when with only seconds on the clock, captain Gifton Noel-Williams forced a corner with his 20-yard deflected shot.
However, it wasn't to last long as the visitors gained a strong foothold through striker Cameron Jerome.
After a left-sided Joe Ledley cross, the youngster's looping header almost beat Steve Simonsen with the ball clipping the crossbar.
The opener came on 26 minutes when a poor pass by Gerry Taggart fell to the feet of former fellow employee Peter Thorne.
His pass picked out Jerome and left him to calmly slot the ball into Simonsen's bottom left from 12 yards.
An equaliser came five minutes before the break when Clint Hill took full advantage of a 25-yard free-kick to score his first for the club.
A lay-off by Dave Brammer was met by the boot of the defender to send his strike into Neil Alexander's bottom left corner.
The Potters should have taken the lead four minutes after the restart but a blunder by Noel-Williams prevented the opportunity.
After a superb header by on-loan Kenwyne Jones, City's leading scorer seemed to clear his team-mate's effort over the bar.
The Bluebirds soon found their rhythm again though and on 58 minutes retook a slender lead.
Another defence-splitting pass by Thorne found Jerome who this time opted to cheekily chip the ball over the sliding Simonsen.
Only two minutes later another defensive error, this time by Lewis Buxton resulted in a penalty when he fouled Jobi McAnuff.
Thorne had no reservations and stepped up confidently, stroking the ball into the despairing Simonsen's bottom right corner.
Late changes in desperation made little impact as Stoke's lowest crowd of the season waved goodbye to their play-off hopes.