Spaniard Toni Elias finished second for Honda, edging out Stoner's Ducati team mate Loris Capirossi of Italy.
The 21-year old Australian rookie will replace the Spaniard for next season's MotoGP campaign, the team confirmed.
Ducati's Loris Capirossi stormed to victory in the Japanese Grand Prix, with champion Valentino Rossi finishing second.
Italian Loris Capirossi won the MotoGP Czech Grand Prix after leading from start to finish.
The 21-year-old Australian started third on the grid but he surged into the lead on the first lap and never lost it, easing to his ninth victory of the season.
Valentino Rossi crashed out of the Japanese Grand Prix as fellow Italian Max Biaggi finished second.
Valentino Rossi made it five MotoGP wins in a row at the Italian Grand Prix
Former MotoGP rider Capirossi pleased with BIC ahead of inaugural race
Italian racer Doriano Romboni died on Saturday after being struck by another rider's bike at an event in memory of late compatriot Marco Simoncelli, who was killed in a similar fashion two years ago.