Lorenzo beats Rossi for Motegi victory.

Jorge Lorenzo held off team-mate Valentino Rossi to win an action-packed Japanese Grand Prix at Motegi, the 700th premier-class race to be held since 1949.

Grid positions had been decided by free practice times after a qualifying wash-out, with Sunday's extended morning warm-up then rendered useless - in terms of dry race preparation - by another heavy shower.

That meant riders began the race with only 45 minutes of dry set-up time, from Friday afternoon, under their belts - prompting Rossi to predict that the race would be "the most uncertain ever".

Rossi made an unusually fast start from pole to lead Chris Vermeulen and Dani Pedrosa - just eleventh on the grid - through turn one, with Qatar winner Casey Stoner dropping from second to fourth ahead of Lorenzo and Andrea Dovizioso.

Pedrosa and Lorenzo overcame Vermeulen's Suzuki on the opening lap, with Jorge then overtaking Pedrosa's Repsol Honda on lap three and instantly biting a half second chunk out of Rossi's lead.

By lap eight of 24 Lorenzo was just 0.2sec behind the leading Fiat Yamaha and ready to strike. The Spaniard's first attempt was unsuccessful, but Rossi was helpless to prevent the #99 from out-braking him at the end of the back straight later on lap nine.

Lorenzo and Rossi remained in close formation until Rossi suffered problems on lap 15, and the resulting 'moments' suddenly handed Lorenzo a 1.5sec lead.

Rossi was now in real danger of losing second to Pedrosa, who had surprised even himself by keeping pace with the leaders despite his diminished physical condition following last month's knee and forearm surgery.

Dani made a lunge for second with eight laps to go, triggering an entertaining series of passes and re-passes between himself and Rossi. The Doctor ultimately prevailed and went on to enjoy a late race resurgence, closing back in on Lorenzo to keep pressure on the 22 year-old.

Nevertheless, Lorenzo didn't put a wheel wrong and collected his second MotoGP victory by 1.3sec from Rossi in Yamaha's home race, while Pedrosa crossed the line 3.8sec from victory for an impressive first podium of the season.

Honda had been facing an embarrassing home weekend - in the 50th year since its grand prix road racing debut - when the top RCV, of Pedrosa's team-mate Andrea Dovizioso, was only seventh in Friday practice, at a track built and owned by Honda.

However, race day was far more fruitful, with Dovizioso also running with the leaders for much of the race on his way to a Qatar repeat of fifth position.

Between the two RCV riders was 2007 world champion Stoner. The Ducati Marlboro star began the race between Rossi and Lorenzo, but was initially unable to match the leading pace.

The Australian spent much of the race in fifth, before getting the better of Dovizioso with three laps to go.

A distant sixth place went to Marco Melandri, who pulled off another giant killing performance on his unofficially backed Hayate. The Italian held his eighth place on lap one, then spent much of the first 10 laps battling with Vermeulen and Stoner, before settling in to sixth.

Vermeulen steadily dropped back from his strong start and was eleventh by the midway point, before gaining one place at Randy de Puniet's expense. By contrast, team-mate Loris Capirossi fought forward from a poor start to take seventh, and his first finish of the season.

Mika Kallio was once again the top rookie, replicating his eighth in Qatar for Pramac Ducati despite starting just 17th - and with a sore ankle - following a Friday fall.

James Toseland finished one place higher than he'd qualified, in ninth, while team-mate Colin Edwards, fastest in the wet on Saturday morning, raised his hand during lap one to indicate some kind of technical problem with his Monster Yamaha.

The Texan had soon dropped to the back of the field, but his persistence in remaining out was rewarded with twelfth position.

Nicky Hayden's miserable start to his Ducati career continued at Motegi, albeit through no fault of his own.

The American was hit from behind by home rookie Yuki Takahashi on lap one, leaving both riders down and out - and Hayden, who sustained a back injury in qualifying at Qatar, in visible pain. Takahashi's body language indicated he accepted full responsibility for the incident.

Other fallers were Spaniards Sete Gibernau and Toni Elias, both of whom remounted although only Elias reached the flag, in 15th and last for Gresini Honda.

Lorenzo's 3-1 results mean he now leads Rossi (2-2) by one point in the world championship standings heading into his home Spanish Grand Prix at Jerez next weekend, the first European round of the 2009 season. Stoner is three points from the top in third.

Japanese Grand Prix:

1. Lorenzo
2. Rossi
3. Pedrosa
4. Stoner
5. Dovizioso
6. Melandri
7. Capirossi
8. Kallio
9. Toseland
10. Vermeulen
11. de Puniet
12. Edwards
13. de Angelis
14. Canepa
15. Elias