Stoner raised his world championship lead to a near unstoppable 60 points over the Italian, with six rounds remaining, by shrugging off the early challenge of Rizla Suzuki's
John Hopkins, then delivering the kind of peerless race pace suggested by his practice times.
By the midway point of the 22 laps, Stoner sat 2.496secs clear of Hopkins - but that extended to 7.903secs by the chequered flag. Nevertheless, second place marked Hopper's best ever
MotoGP result and only his second grand prix podium after Shanghai earlier this season.
Third position went to outgoing world champion
Nicky Hayden - who had qualified second to Stoner, slipped to fourth at the start, but then muscled past Repsol Honda team-mate
Dani Pedrosa for third place on lap two - a position he held to the end for his third 800cc podium.
Top Michelin rider Hayden crossed the line five seconds from Hopkins and almost three seconds in front of a frustrated Pedrosa, who quickly departed after returning his RC212V to the pits.
The fight for fifth was more intense, with
Chris Vermeulen carving his way from the lower reaches of the top ten to sixth, a fraction behind Rossi, by the halfway stage. Fifth was as high as Rossi rose on Sunday and he lost the position to the Australian on lap 13, then fell victim to
Loris Capirossi's powerful Ducati three laps later.
Another
Bridgestone rider, Kawasaki's
Randy de Puniet, was also queuing up to pass the #46, who seemed to once again be battling tyre troubles - in addition to his much publicised off-track tax problems. Fortunately for Rossi, de Puniet lacked the decisiveness to make a pass - leaving the Italian seventh at the flag, 22 seconds from Stoner, and de Puniet half a second further adrift.
Alex Barros rode a strong come-from-behind race to claim ninth for d'Antin Ducati, while Honda LCR's Carlos Checa got the better of a healing
Toni Elias for tenth.
Elias' Gresini Honda team-mate
Marco Melandri missed the race due to a neck hernia, while
Colin Edwards was the only non finisher after falling from his Fiat Yamaha early in the grand prix.
Czech Grand Prix:
1. Stoner
2. Hopkins
3. Hayden
4. Pedrosa
5. Vermeulen
6. Capirossi
7. Rossi
8. de Puniet
9. Barros
10. Checa
11. Elias
12. West
13. Guintoli
14. Nakano
15. Roberts
16. Silva
17. Tamada
