Ducati Marlboro rider Casey Stoner finished fourth. Pedrosa's team-mate Andrea Dovizioso came in fifth while Britain's James Toseland on the Yamaha Tech 3 came in a disappointing ninth.
Spaniard Lorenzo, started on the front row at the Twin Ring Motegi, with Stoner and Rossi, who had clinched pole position after heavy rain washed out the previous days qualifying session. Shades of Qatar were looming, but the weather held for the main twenty four lap race as Rossi led for the opening eight. Once Lorenzo wriggled passt the Italian he managed to hold the lead over the Rossi and Pedrosa, leaving them to fight it out for second and third place. The margin between the Spaniard and the Italian at the line was a mere 1.304 seconds.
Lorenzo now heads up the standings on 41 points with Rossi on 40, 2 ahead of Australian Stoner.
In the 250cc classification, Spaniard Alvaro Bautista claimed first place on his Aprilla, 5.8 seconds ahead of Honda rider Hiroshi Aoyama in second and a massive 22 seconds ahead of Italian Mattia Pasini also riding an Aprilla.
First and second places in the 125 cc classification went to Aprilla Riders Andrea Lannone from Italy and Spaniard Julian Simon respectively. Simons countryman Pol Espagaro came third riding a Derbi.
The second round of the 2009 Moto GP motorcycle racing season, the Japanese motorcycle Grand_Prix turned out to be a thriller and certainly a lot less wet than the rain affected meeting in Qatar.
The race was won by Jorge Lorenzo who took the chequered flag on his Fiat Yamaha just over a second ahead of his team-mate Valentino Rossi, with Dani Pedrosa coming in third place.
