That position eventually went to Tech 3's Colin Edwards, who finished four seconds from Pedrosa and two seconds in front of Dovizioso, despite having been just seventh at the end of lap one.
Hayden, who had been rejuvenated by the chance to finally ride Honda's pneumatic-valve engine at a race weekend, briefly rose to third on the opening lap - and was still fourth by the halfway stage - but his concerns over how the new engine would react over a full distance seemed justified as he dropped back to seventh at the chequered flag.
After qualifying on the front row for the first time this year, Rizla Suzuki's Chris Vermeulen hung on to sixth for much of the race, but lost out to Lorenzo and Hayden in the closing stages.
Reigning double AMA Superbike champion Ben Spies, who qualified an excellent eighth in the rain - the best premier-class debut by an American since John Kocinski qualified 8th for the 1989 Belgian Grand Prix - brought the second GSV-R home in 14th position to score his first world championship points at his first attempt.
Having qualified a disastrous 16th on the grid, following two falls at the end of qualifying, things quickly went from bad to worse for home hero James Toseland - who highsided from his Tech 3 Yamaha at the first turn of his first British Grand Prix.
Few would have blamed the reigning double World Superbike champion, who seemed to suffer a hand injury in the spill, if he had called it a day there and then, but the #52 got back on his damaged bike and took it to the chequered flag one lap down in 17th position.
Anglo-American John Hopkins was held up by Toseland's fall, but fought his way aggressively back up to tenth - only for his Kawasaki to suffer a terminal technical fault for the third time this season.
Team-mate Anthony West enjoyed his best race of the season to eventually take tenth position, at a track he made his ZX-RR debut at one year ago, but Stoner's team-mate Marco Melandri saw no such light at the end of the tunnel.
The Italian finished 16th, one place behind rookie Alex de Angelis - even though the Honda Gresini rider fell at the Melbourne Hairpin on lap two and rejoined behind all but Toseland.
Round nine of the 2008 MotoGP World Championship, the Dutch TT at Assen, takes place next Saturday.
British Grand Prix:
12. de Puniet
15. de Angelis