The Senegal international ran 80 yards with the ball to score the only goal of the game as Potters boss Mark Hughes handed his former club their first defeat of the season
A lethargic City performance was punished on 58 minutes when Diouf raced upfield from a defensive corner and beat Fernandinho before firing through the legs of a sprawling Joe Hart.
Manuel Pellegrini's men pushed hard for an equaliser in the closing stages but a combination of poor finishing and dogged defending saw the Potters hold out for the win.
|VIEW FROM THE ETIHAD
|By Paul MacDonald
Manchester City only failed to score once at home in the entirety of last season, but just two games into the new campaign and they have looked far from impressive against a well organised Stoke side that were well worth their win.
David Silva was on the periphery, Yaya Toure was subdued and Samir Nasri anonymous.
Once behind to Mame Diouf's sensational solo goal there was no City onslaught, no expected siege in the final moments.
In truth, it was arguably the poorest performance Manuel Pellegrini has overseen since arriving here last summer. Much to ponder for the Chilean - this simply wasn't good enough.
The hosts were given an early scare when Sergio Aguero collided with Ryan Shawcross, although the Argentine striker was quickly back in action after receiving treatment.
Aleksandar Kolarov then connected with David Silva's cross and saw his header drift marginally off target before Steven N'Zonzi shot high and wide to conclude Stoke's first dangerous foray forward.
Stoke gradually grew into the game and were denied a penalty 18 minutes in when Diouf went down in the area after evading Kolarov.
Lee Mason waved away the protests and the referee was soon required to cool an off-the-ball incident between Shawcross and Stevan Jovetic that capped a scrappy opening half-hour.
Pellegrini replaced the injured Fernando with Fernandinho, before Yaya Toure clipped the crossbar with the final effort of the opening half.
Diouf was again left frustrated when Mason denied him a penalty early in the second half, while Samir Nasri saw a shot deflected wide after good interplay between the Frenchman and Silva.
As in the first half, Stoke's deep and resolute backline proved difficult for the home side to break down.
A curled effort from Toure was beaten away by Begovic, before the lively Diouf gained reward in the 58th minute when he surged forward from inside his own half and nudged the ball past Fernandinho.
Having burst into the area, Diouf tucked the ball past Hart - who will perhaps feel he should have done better - and opened his account for Stoke.
While the home side rallied, it was Stoke who had the better chances to extend their lead as Victor Moses came close to connecting with Peter Odemwingie's cross and Peter Crouch headed wide.
City had a late shout for a spot-kick turned down when Erik Pieters carelessly tangled with Toure but Mason again opted to wave play on and Stoke secured three hard-earned points.