It was harsh on City who, despite being the better team for much of the game, fell behind to a late Dave Kitson goal only to level within two minutes through Craig Bellamy.
Looking likely to go on and win the tie, the Blues were then reduce to ten men when Emmanuel Adebayor was controversially shown a straight red card by referee Steve Bennett for appearing to catch Ryan Shawcross in the face, though the decision appeared harsh at best.
Now the Blues will need to pick themselves up quickly with a crucial Premier League fixture at Chelsea to come this weekend.
On yet another freezing night in Staffordshire, it was the hosts who came into the game in better form, having failed to lose a game in 2010.
Unbeaten in ten matches in all competitions, only Birmingham City had left the Britannia with a victory in the previous 11 home games.
Indeed, with Chelsea waiting in the last eight, Stoke may not reach the FA Cup final this season, but they tend to treat every game they play at home like a cup final and love or hate their style, when it works, there’s no arguing over its effectiveness.
As for City, Roberto Mancini had promised his team would fight fire with fire in order to emerge from this game with a victory, but few teams fan the flames quite as vehemently as Tony Pulis’ side.
There were a number of surprises in Mancini’s starting XI with Nedum Onuoha drafted in for his first start since the trip to Scunthorpe last month and Micah Richards returning at right-back.
Pablo Zabaleta and Vincent Kompany were moved into a new-look midfield at the expense of Nigel de Jong and Shaun Wright-Phillips who both dropped to the bench.
Bellamy replaced the cup-tied Adam Johnson while the Potters were without suspended pair Andy Wilkinson and skipper Abdoulaye Faye.
The changes worked well, too, particularly in the first half when, on another night, the Blues could easily have gone in 4-0 up at the break after dominating proceedings.
The impressive Adebayor was the first to go close when, on seven minutes he launched a 25-yarder that Thomas Sorensen did well to keep out and both Kompany and Onuoha saw efforts go the wrong side of the post with game barely 15 minutes old.
The best opportunity of the opening period, however, came on 19 minutes when Adebayor judged the bounce of a Shay Given clearance better than the Stoke defence to race towards goal but when he played in Bellamy, the Wales striker shot straight at Sorensen
After surviving the first 45, Stoke re-grouped after the break and were marginally the better side, without ever really troubling Given.
In fact, as the game entered its latter stages, it seemed unlikely anyone would score during normal time - until sub Kitson’s 79th-minute strike from 10 yards found the bottom corner of Given’s net.
Down but not out, the Blues equalised two minutes later when Adebayor’s smart lay-off found Bellamy who fired a low drive past Sorensen to make it 1-1 and send 4,000 travelling fans into raptures.
The pivotal moment of the match, however, came shortly after when Adebayor appeared to shrug off Shawcross’ fussy marking with a flailing arm and earn himself a straight red.
From that moment on the Blues, who may well have gone on to win the game with a full quota of players, faced an uphill battle and as the game went into extra time, Stoke upped the ante.
With the home fans urging their team to move in for the kill, extra time goals from Shawcross and Tuncay sent the Tony Pulis’ side into the last eight.
