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The Potters were the first team in 12 to emerge victorious after using the South dressing room at the impressive stadium thanks to a close-range strike by Deon Burton and a Ben Burgess own goal.
The first goal came in the 16th minute when Chris Iwelumo flicked on Arnar Gunnlaugsson's corner and Burton was given time and space to control the ball before firing his shot past Paul Smith in the Bees goal.
It was the Jamaican international's fourth goal for Stoke since his loan move from Derby County.
Steve Coppell's side hit back well though and Burgess fired wide before Steve Sidwell shot over the bar from a good position.
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However, Brentford were dealt a major blow just before the break when Bjarni Gudjonsson's free-kick was turned into his own net by the unfortunate Burgess.
It could have been even worse for Brentford as in first-half stoppage time Tony Dinning's rasping drive was fortuitously turned over the crossbar by Smith.
After the interval Stoke appeared content to hang on to their lead and although Lloyd Owusu and Paul Evans went close for the Bees, the West London side looked lightweight up front.
Their best chance came with nine minutes left when Mark McCammon's close-range header was somehow kept out by Neil Cutler.
However, Stoke deserved their success which seemed highly unlikely when they trailed 2-0 at home to Cardiff City in the semi-final first leg at the Britannia Stadium.
A late Burton goal then and a famous 2-0 victory at Ninian Park ensured Stoke progressed to the final and the Potters can now look forward to a return to the first division after a four-year absence.
The victory tasted especially sweet as they had lost out in the play-offs in each of the last two seasons.