The Repsol Honda rider, who trails the factory Yamaha of defending champion Jorge Lorenzo by seven points in the championship standings ahead of tomorrow's sixth round of the series, was quickest in the final practice session with a time of 2min 15.666sec at the Northamptonshire circuit.
Stoner swapped top place on the timesheets several times with the San Carlo Gresini Honda of Marco Simoncelli before exerting authority towards the end.
Second fastest time was still a good result for Simoncelli who has courted controversy this season as his aggressive riding style.
Nicky Hayden was a surprise third quickest on the factory Ducati ahead of Britain's Cal Crutchlow on the Monster Tech 3 Yamaha.
Lorenzo was a disappointing fifth, with Repsol Honda's Andrea Dovizioso in sixth, Ben Spies (Yamaha) seventh and Cardion Ducati's Karel Abraham in eighth.
Multiple world champion Valentino Rossi (Ducati) was down in ninth and LCR Honda's Toni Elias rounded out the top ten.