Dani Pedrosa handed Honda a home win in an eventful and attritional race at Motegi, which counted Ducati's Valentino Rossi as one of its several victims.
Pedrosa's route to the front happened more by fortune than design, as accidents dominated the Japanese Grand Prix.
Rossi was the first casualty, as he made contact with Lorenzo at Turn 2 on the opening, losing the front end and also collecting Yamaha's Ben Spies as he slid into the gravel and out of the race.
Stoner meanwhile had protected his lead and rapidly built a lead of more than 1s, but on lap four suffered a huge wobble over the back straight bumps and missed his braking point into Turn 11 - running through the gravel and dropping down to seventh as a result.
The lead therefore transferred to Andrea Dovizioso, who had passed his Honda team-mate Pedrosa in the opening stages.
Dovizioso however was one of three riders adjudged to have jumped the start, and on lap five came into the pits for his ride-through - Gresini's Marco Simoncelli and Tech 3's Cal Crutchlow following him in after also falling foul of the stewards.
Victory became a straight fight between Pedrosa and Lorenzo, and a series of fastest laps was enough to earn the Honda man his third win of the year.
As he did so, Motegi claimed another two victims. Hayden ran deep and through the gravel at Turn 1 while trying to follow Stoner, while several laps later Bautista made a mistake of his own accord, losing the front of the Suzuki at Turn 12 and crashing out from fourth.
Dovizioso and Simoncelli meanwhile had fought their way back through the field, and the Gresini rider claimed fourth one lap from the end with a typically aggressive pass at Turn 11.
Having fallen on the opening lap incident with Rossi, Spies capped a fine comeback ride by finishing sixth, ahead of Hayden and Tech 3 Yamaha's Colin Edwards.
Toni Elias on the LCR Honda had held sixth but crashed with just seven laps to go, while on his MotoGP debut Damian Cudlin (Pramac Ducati) was another Motegi casualty, crashing out just after the half-distance mark.