“Today was very tough because Jorge had a fantastic rhythm in practice,” said Rossi. “When he overtook me I was ready for the battle, but after he lost the front and it is very bad for Jorge, it is a pity, but it is good for us. There is a long way to go but it is a good advantage.”
Last year at Brno Elias had finished a distant second to Rossi after Stoner's exit. This time the Spaniard - out of ride with Honda Gresini at the end of the season - was able to claim third place after a thrilling battle with Andrea Dovizioso. The result marked Gresini's first podium since Marco Melandri in 2007.
Melandri, who will return to Gresini next season, didn't reach the finish after a spectacular clash with Mika Kallio on the penultimate lap. The Italian divid inside Kallio, replacing the absent Stoner at Ducati Marlboro, for eighth through the final chicane, but the pair slammed into each other as their lines crossed on the exit.
Bikes and riders tumbled together through the gravel, before a furious Kallio confronted an equally angry Melandri.
Loris Capirossi rode a solid race to fifth for Suzuki, just 0.12sec behind Dovizioso, while Nicky Hayden took a significant step towards a new Ducati contract with sixth position - one place off his best result of the season - having been ahead of Kallio throughout the race.
Colin Edwards had hoped he could battle Pedrosa for what looked like being third, before the race, but instead had to be content with seventh for Monster Yamaha Tech 3.
Second Gresini rider Alex de Angelis and Edwards' team-mate James Toseland were eighth and ninth, while Randy de Puniet rode through the pain from his broken ankle for tenth for LCR Honda.
Chris Vermeulen (Rizla Suzuki), Niccolo Canepa (Pramac Ducati) and Gabor Talmacsi (Scot Honda) completed the finishers.
WSBK star Michel Fabrizio, subbing for Kallio at Pramac Ducati, retired on lap 6 with some kind of arm problem. 250GP race winner Mattia Pasini will test for the team on Monday and is favourite to get the ride at Indianapolis.
Brno marked the start of new engine regulations, which allow a maximum of five engines changes to be made by each rider during the final seven rounds of this season. Extra engine changes are punishable by a ten point penalty.
In 2010, the rules will demand further increases in engine life with each rider being limited to six engines for the whole 18-race series.
A test session takes place at Brno on Monday before round twelve of the 2009 MotoGP World Championship is held at Indianapolis on August 28-30.
Czech Republic Grand Prix:
8. de Angelis
10. de Puniet