MATTHEW Etherington's debatable 55th-minute penalty set Albion on their way to an undeserved second successive home defeat.
TV replays suggested Scott Carson failed to make contact with Kenwyne Jones when the Sunderland striker went to ground in the box - but referee Chris Foy pointed to the spot.
A second penalty for City five minutes from time was just as contentious.
This time sub Simon Cox was adjudged to have fouled Dean Whitehead when it looked nothing more than a shoulder-to-shoulder challenge and Jon Walters stepped up to seal City's third consecutive win from 12 yards.
Sub Walters' second in the third minute of stoppage time rubbed even more salt into Albion wounds.
City boss Tony Pulis has been very vocal in recent weeks regarding harsh refereeing decisions going against his team - but the tide certainly turned in his favour today.
The result was rough justice on Roberto Di Matteo's men, who comfortably dealt with the little threat the visitors offered and asked most of the questions.
Giles Barnes was handed his first Barclays Premier League start for the Baggies as Di Matteo made three changes - one enforced.
The former Derby midfielder replaced the injured Chris Brunt (groin) while Marek Cech and the back-from-suspension Gonzalo Jara came in for Nicky Shorey and Steven Reid.
Pulis named an unchanged XI from last weekend's 2-0 home win over Liverpool.
The teams were only separated by goal difference before kick-off as 12th entertained tenth.
Albion started brightly and Danny Collins had to produce a vital block after only 44 seconds when Peter Odemwingie turned sharply from Barnes' low centre and fired goalwards.
The game soon settled into a cat-and-mouse affair as Stoke sat back and the Baggies prodded and probed to find a way through the red-and-white defensive wall.
Stoke suffered an injury set-back after only 11 minutes when Jermaine Pennant limped off and was replaced by Tuncay.
Albion comfortably dealt with a couple of Rory Delap's trademark throw-ins and in a game of few chances thus far, Asmir Begovic was well positioned to grasp Odemwingie's ambitious 30-yard drive.
The patience the Baggies were having to show in possession wasn't lost on the home hordes and one slick passing move ended with Youssouf Mulumbu sending a terrific 25-yard drive just over.
Albion began to turn the screw as Barnes came to life.
After skipping past Collins down the right, his vicious cross wreaked havoc in the City box and a better ball from Jerome Thomas would have provided James Morrison with a simple chance.
Mulumbu then teed Barnes up in the box and his cross looked destined for Morrison's head at the back stick - until Ryan Shawcross flicked it away in the nick of time.
City still hadn't had an effort at goal when Odemwingie whipped a free-kick on the edge of the box a yard over Begovic's bar on 39.
The Nigerian was determined to break the deadlock and, just two minutes later, he teased his way past several Stoke defenders before losing his footing at the vital moment and seeing his effort dribble into Begovic's arms.
The second half followed a similar pattern, with Albion on the front foot but finding it difficult to crack Stoke's stubborn rearguard action.
But the game turned on a highly controversial moment in the 55th minute.
Carson came racing off his line to close down Jones who had been fed in the box by Ricardo Fuller and the Albion skipper appeared to fail to make contact with both the ball and player.
But the Sunderland striker hit the deck and referee Foy pointed to the spot.
Etherington made no mistake from 12 yards, tucking the ball calmly into the bottom right-hand corner.
That was Stoke's first shot at goal and they soon recorded a second, when Jones fired straight at Carson from 20 yards.
The goal had knocked the stuffing out of the hosts but Whitehead was well off target with a speculative 20-yard volley.
However, the introduction of Somen Tchoyi on 66 breathed new life into Albion.
And moments after his low cross somehow evaded several team-mates inside the penalty area, the Cameroon international teased his way past Collins before forcing a fine near-post save out of Begovic.
Another sub, Cox, spread the ball wide to Thomas who skipped past Andy Wilkinson and his cross was headed goalwards by Tchoyi, who again was denied by Begovic's finger-tips.
Seconds later, Cech powered forward and fired just over from the edge of the box.
Albion now had Stoke firmly on the back foot and Cox saw a 30-yard effort deflect off a Potters defender and fly just wide.
But Stoke were awarded a second penalty five minutes from time when Cox was adjudged to have fouled Whitehead and this time sub Walters beat Carson from 12 yards.
Albion still refused to lie down and Ibanez was denied at point-blank range by Begovic before the Spaniard headed over from Odemwingie's rght-wing cross.
Begovic then had to be alert to rush off his line and save at Cech's feet as he attempted to connect with sub Graham Dorrans' through-ball.
Cech went even closer moments later when he fired over from 12 yards after Odemwingie's blocked shot had fallen neatly into his path.
But, incredibly, it was Stoke who finished off the scoring in ultimate smash-and-grab fashion.
In the last minute of stoppage time, Jones back-heeled the ball to the Republic of Ireland international whose initial effort was brilliantly saved by Carson but he fired the rebound into the roof of the net.
ALBION (4-2-3-1): Carson; Jara, Ibanez, Tamas, Cech; Scharner, Mulumbu (Dorrans 80); Barnes (Tchoyi 66), Morrison (Cox 56), Thomas; Odemwingie. Subs not used: Myhill (gk), S Reid, Shorey, Fortuné.
STOKE (4-4-2): Begovic; Wilkinson, Huth, Shawcross, Collins; Pennant (Tuncay 11), Delap, Whitehead, Etherington (Walters 78); Fuller (Wilson 83), Jones. Subs not used: Sorensen (gk), Higginbotham, Whelan, Gudjohnson.
GOALS: STOKE - Etherington (pen 55), Walters (pen 85, 90+3).
REFEREE: C Foy (Merseyside).
ALBION STARMAN: Gabriel Tamas.
PIC: AERIAL ACTION...Ibanez tussles with Fuller