The Rossi/Stoner collision left Simoncelli, without even a MotoGP podium to his credit, holding a two-second lead - but the Italian threw it all away when he lost the front, then the rear, and highsided out at turn one on lap 12.
That handed Lorenzo a lead he held to the flag, but not before successfully responding to pressure from countryman Dani Pedrosa, who closed almost to within striking distance of the Yamaha rider before losing pace.
It looked like Pedrosa was suffering a repeat of his arm numbness problems as he slipped back into the clutches of Lorenzo's team-mate Ben Spies late in the race.
However, tyre wear seems to have been the critical factor for all riders in the closing stages - and cost two competitors a place on the podium.
Spies, having overtaken Pedrosa on lap 24, then crashed out of second on the following lap.
That mistake handed fellow American Colin Edwards the final podium place, the Monster Yamaha Tech 3 rider having just overtaken Hayden, but a stunned Edwards then crashed out after a technical failure on the last lap!
Hayden thus picked up Ducati's first podium of the season, from eleventh on the grid, with Hiroshi Aoyama just behind him. Rossi was over 1 minute from Lorenzo, who once again celebrated by jumping into a lake.
Rookie Cal Crutchlow was another victim of the grip levels, falling from his Tech 3 bike while fifth with seven laps to go – the Englishman rejoined to finish eighth behind Hector Barbera and Karel Abraham. Abraham also fell during the race.
The rate of attrition helped LCR Honda's Toni Elias claim ninth and John Hopkins tenth in his first MotoGP race since 2008, as a replacement for the injured Alvaro Bautista at Rizla Suzuki.
Loris Capirossi was the only Pramac rider to finish, in eleventh - after a crash for Randy de Puniet - while third Repsol Honda rider Andrea Dovizioso, who ran off track, made a pit stop on his way to twelfth and last.
Pedrosa will undergo shoulder surgery on Monday to try and cure the numbness he has suffered since his collarbone was broken at Motegi last year.