SALIF DIAO'S first goal for the club was enough to ensure all three points for the Potters and extend their unbeaten run to ten games.
The former Liverpool man had only been on the pitch for ten minutes when he smashed home from close range in stoppage time after Ricardo Fuller brilliantly teed him up.
City had Robert Huth to thank for getting them back in the encounter after the German international ruled out Frederic Piquionne's first half strike with a well taken header just five minutes into the second period.
The win was even more superb due to the fact they were forced to play the final 20 minutes with ten men after Andy Wilkinson was controversially sent off after receiving two yellow cards.
Ahead of the game Tony Pulis made three changes to his starting line-up with Tuncay, Andy Wilkinson and Danny Collins all handed starts at the expense of the suspended Abdoulaye Faye, the injured Danny Higginbotham and Liam Lawrence.
The hosts made a number of changes themselves as they handed a debut to new signing Quincy Owusu-Abeyie as part of a three man attack, which also featured Ivorian Aruna Dindane and Frenchman Piquionne.
The first half was a largely lethargic affair with neither side really able to impose themselves on the game. A number of trademark Rory Delap long throw-ins caused brief moments of panic inside the Pompey penalty box early on, whilst on loan Spurs man Jamie O'Hara rifled well wide from 15-yards.
The first real effort of any note fell to Piquionne midway through the half after he cleverly dinked the ball over Thomas Sorensen after being played through by O'Hara, however, his strike was chalked off after the linesman adjudged him to have been offside.
The on loan striker was soon in the thick of the action again and did manage to punish the Potters by firing the hosts in to the lead when he reacted quickest to turn the ball into the back of the net after Owusu-Abeyie saw his strike palmed away by Sorensen.
Right on the stroke of half time Turkey star Tuncay had a glorious opportunity to level the scoreline, but he headed wide of the post after Whelan had picked him out with a delightful ball.
Avram Grant was handed a blow during the interval as the impressive Piquionne was forced to withdraw after pulling up with a tight hamstring. His replacement came in the shape of former Arsenal star Kanu, and he was immediately stirring things up with his trickery.
In fact the Nigerian won the hosts a corner a minute into the second half which forced Wilkinson into making a superb last ditch header to deny the fast approaching Dindane.
Four minutes later though the game was all square. Republic of Ireland international Whelan delivered a delightful corner straight into the path of Huth, who rose highest and powered the ball into the roof of the net leaving James helpless.
One almost became two as the Potters caught Pompey off guard with a superb counter-attack.
Tuncay picked the ball up in his own half and set off on a darting run deep into the oppositions half, however, with Fuller crying out for the ball to his left he opted to strike and the ball was blocked.
The danger didn't end there as Delap picked up the loose ball and cannoned an effort goalwards which James brilliantly saved at his far post.
Both sides then exchanged blows with Whelan and Fuller firin over for the Potters whilst substitute John Utaka and midfielder O'Hara warmed the hands of City's Danish international goalkeeper.
Pulis' hopes of securing maximum points, or even one point for that matter, were dealt a huge blow with just under 20 minutes remaining as Wilkinson was harshly adjudged to have pulled down Dindane on the flank, prompting referee Mike Dean to dismiss the unlucky defender.
Despite battling with ten men the Potters continued to look the side more likely to get the win, and they reaped their rewards in the first of four minutes of added time when Diao struck home after brilliant work from the lively Fuller.
The win means the Potters are now level on points with Fulham in tenth place, whilst it also represent the first win from coming from behind since winning promotion to the Premier League almost two years ago.