The MotoGP rookie attempted to re-fire his Fiat Yamaha with a bump start, doing little to reduce the pain from his injured ankles, before getting assistance from officials and taking his fourth place on the grid.
The Spaniard, who celebrated his 21st birthday today, looked understandably cautious in the early stages - and had been mercilessly pushed back to eighth by the halfway mark - but retaliated with a combative performance during the last ten laps to pull a comfortable 4.4secs clear of fifth place.
The tailwind on the back straight contributed to a multitude of braking mistakes into the ultra-tight hairpin, with pole sitter Colin Edwards one of the most high profile victims.
The Texan swapped the lead with Stoner during the opening laps but - having been passed by Rossi and Pedrosa - had looked more than capable of holding third, until he ran wide on lap 6.
That dropped the Tech 3 Yamaha rider to seventh, where he eventually finished - in the middle of a close five-man pack - behind Marco Melandri and Nicky Hayden, and ahead of Toni Elias and Loris Capirossi.
Melandri delivered by far his best race of the season, the Italian looking like a man transformed as he charged from 12th on the grid to fifth, shattering his previous best race finish of eleventh and releasing some of the huge pressure on his shoulders after a nightmare start to his Desmosedici career.
Capirossi was the only Rizla Suzuki rider to reach the flag after Chris Vermeulen retired with chain problems, whilst James Toseland endured his toughest MotoGP race yet - crossing the line in twelfth, albeit just a fraction behind fellow rookie Andrea Dovizioso, who faded backwards in the closing stages.
Kawasaki endured a race to forget, John Hopkins managing just 14th after several mistakes whilst trying to force his way forwards from 12th on the grid, while team-mate Anthony West finished in a distant last place - where he had started.
In the world championship standings, Pedrosa has now broken seven points clear of Lorenzo, with Rossi just two points behind his team-mate in third. Stoner remains fourth, but has slipped 25 points - one race win - behind Pedrosa.
Sunday's race was rumoured to be the final Chinese Grand Prix for the foreseeable future - a new round in Hungary, feeding on the huge support for 125cc world champion Gabor Talmacsi, is tipped to replace the Shanghai event from next season.
Chinese Grand Prix:
1. Rossi
2. Pedrosa
3. Stoner
4. Lorenzo
5. Melandri
6. Hayden
7. Edwards
8. Elias
9. Capirossi
10. Nakano
11. Dovizioso
12. Toseland
13. de Puniet
14. Hopkins
15. Guintoli
16. de Angelis
17. West