Roberto Mancini's men lifted the FA Cup to end a 35-year wait for a major trophy.
Toure got the all-important goal after pinball in the Stoke area, with team-mates David Silva and Mario Balotelli also involved.
Toure smashed the ball home after it was deflected to him by Marc Wilson and that was enough to give his side victory.
Almost three years after Sheik Mansour's takeover transformed Man City into one of the richest clubs in the world, his £300million investment has now produced Champions League qualification and an FA Cup triumph in the space of a week.
It was somehow fitting that semi-final hero Yaya Toure - reportedly the highest paid player in the Premier League on £185,000 a week - was the match-winner again on Saturday. Stoke's 148-year wait for FA Cup glory goes on.
Man City had not won the cup themselves since 1969 but the Potters had not even been to a final and were the only surviving founder members of the Football League never to lift the trophy.
The 1-0 defeat was also a double-whammy for manager Tony Pulis, whose last Wembley final saw his Gillingham side lose the 1999 Second Division play-offs to Man City.
The build-up to cup final day had been dominated by talk of the competition being further devalued by the scheduling of Saturday's game.
Manchester United clinching the Premier League title minutes before kick-off did not help matters, and neither therefore did a rather unfortunate pre-match rendition of 'We are the Champions'.
But try telling that to the tens of thousands of Man City and Stoke fans crammed into Wembley on Saturday afternoon for what was the first cup final for both clubs for more than a generation.
And try telling it to the managers, who each gambled on the fitness of key players as Carlos Tevez, Matthew Etherington and Robert Huth all started.
Man City captain Tevez soon set about proving manager Roberto Mancini right, forcing a fine parry from Thomas Sorensen from 25 yards.
It was a sign of things to come as Mancini's men belied their reputation for caution in a utterly dominant first-half display.
Ryan Shawcross almost put into his own net and Toure drilled just wide from long range.
And Man City would have been ahead midway through the half but for a world-class save from Sorensen, who somehow clawed behind Mario Balotelli's top-corner-bound curler.
It was looking like Sorensen's lucky day after he kept his place as Stoke's FA Cup goalkeeper ahead of Asmir Begovic.
He survived being beaten to a long ball by Tevez and got away with spilling Vincent Kompany's tame long-ranger.
His luck continued when Tevez brilliantly played in Balotelli and Sorensen beat the ball down straight to David Silva, who rifled a shot into the ground and over the crossbar.
Stoke had gone some way to shattering their own reputation in their free-flowing semi-final demolition of Bolton.
But when Huth's forearm connected with Balotelli's jaw, it was an early indication they had reverted to type.
Long throws and set-pieces were once again the order of the day, although they did fashion a chance in open play when Vincent Kompany threw his body at Kenwyne Jones' close-range shot.
Emerging from what can only have been harsh words at half-time, Stoke tore into Man City early in the second half, Jermaine Pennant playing through the pain of a first-half ankle injury to lead the charge.
But they were unable to produce the finishing touch and were almost caught on the break when Tevez squared for Silva, who hesitated just long enough for Shawcross to nick the ball away.
Joe Hart had been a spectator all afternoon but he came to Man City's rescue just past the hour mark when Jones beat Joleon Lescott to a long ball before poking his finish too close to the keeper.
Etherington, who had looked less than fully fit, was immediately withdrawn for Dean Whitehead.
Mancini responded to Man City's second-half slump by throwing on Adam Johnson for Gareth Barry and it immediately paid off.
City won the ball on the edge of the area and Balotelli exchanged passes via Huth, with the Italian's shot blocked by Marc Wilson straight to Toure to blast home.
Desperate defending and a fine save twice prevented Silva wrapping up victory, with Stoke throwing on John Carew in a bid to keep their dream alive.
Mancini finally went defensive when he withdrew Tevez for Pablo Zabaleta but despite late Stoke pressure, Man City deservedly hung on.