Hayden led Rossi until lap 14 of 20, and his runner-up finish marked his first podium of the year and the first ever for the pneumatic-valve Honda. Problems with the pneumatic during testing meant that it couldn't be used from the start of the season but Hayden, desperate to revive his 990cc form, took a calculated gamble and race-developed the pneumatic as soon as HRC would allow him; from round eight at Donington (two rounds after test rider Tady Okada took the machine to 14th at Mugello).
Hayden's team-mate Pedrosa decided to remain on the spring-valve powerplant until Indy, six rounds after Donington, but a new engine wasn't his only novelty at The Brickyard - Pedrosa was also making his debut on Bridgestone tyres.
Despite eight podiums from the first nine rounds, Pedrosa had lost faith in Michelin by round 13 at Misano - fuelled by ill-suited rubber supplied by the once dominant French manufacturer at the previous Laguna Seca and Brno events.
Those mistakes - which resulted in cut slicks being seen in dry morning practice at Laguna Seca, and world champions Lorenzo and Toseland unable to lap inside the 107% qualifying time at a wet Brno - left many Michelin riders furious and ultimately contributed to the new single tyre rule for 2009.
Nevertheless, most of the paddock was stunned when Repsol and Honda announced on Sunday evening at Misano that Pedrosa - who had just finished fourth in the San Marino GP - would change to Bridgestone tyres with immediate effect. Hayden, heading for Ducati in 2009, was not given the chance to change.
Despite the poor weather at Indianapolis, Pedrosa qualified and finished eighth on his pneumatic/Bridgestone debut, then reassured HRC by claiming his first Bridgestone podium next time out at Motegi.
But the Japanese Grand Prix belonged to Rossi and Yamaha, as The Doctor became only the second rider in history (alongside Agostini) to recapture the premier-class title after two successive defeats, by wrapping up the 2008 world championship in perfect style, with victory in Yamaha's home race at Motegi.
"It's a great victory and a great achievement; I think it's at the same level as the first title in 2004 with Yamaha, maybe even better!" said Rossi. "We have lost for two years and I don't think I was the favourite this season, but we have shown that we are a great team and that we never give up," added Rossi, who celebrated with a t-shirt saying 'sorry for the delay'. "I am so happy that I have now won three titles with Yamaha because this is how many I won with [Honda]. I hope we will have more together! Now I have to get used to being world champion again!"
Stoner, by now diagnosed with a wrist injury that would require a post-season bone graft to fix, may have lost the title, but the young Australian reminded MotoGP of his talents with a home victory at Phillip Island, before Rossi - who had charged from 12th on the grid to second in Australia - claimed his ninth and final victory of the season at the penultimate round in Malaysia.
Sepang was a landmark race for rookie Andrea Dovizioso, who absorbed intense pressure from Hayden - the rider he will replace next season - to claim his very first MotoGP podium.