Dani Pedrosa battled from behind to beat championship leader Jorge Lorenzo at the Japanese Grand Prix on Sunday, stepping up his bid to overtake his fellow Spaniard for his first MotoGP title.

And in further good news for Honda, teammate Casey Stoner retained third place in the standings after finishing fifth.

Stoner missed three races through injury and has no chance of winning the championship but he remains five points ahead of Yamaha's Andrea Dovizioso who finished one place ahead of him on Sunday.

"I'm a little disappointed, to be honest," said Stoner, who turns 27 on Tuesday and will retire at the end of the season.

"At the start of the race I felt I had the pace to stay with Dani and Jorge and the bike was feeling pretty good," he said.

"Then as the race progressed my body started to suffer and ache in ways I didn't expect. We had the pace to run a lot higher and be on the podium but unfortunately I couldn't manage it physically today."

Pedrosa passed pole-sitter and Yamaha ace Lorenzo on the 12th of 24 laps and won by more than four seconds at the Twin Ring Motegi circuit.

Third was Alvaro Bautista on another Honda 2.477 seconds further back.

With his four wins in the past five races, Pedrosa has closed the gap to Lorenzo to 28 points with three races remaining in the season.

"It was a hard race because from the beginning the pace was very fast," said Pedrosa, 27.

"At the beginning, I tried to understand the bike because yesterday it had some chatter (vibration after braking).

"There was one moment I could get right with a right-hand corner so I could pass him and finally I tried to pull some good laps," he said.

"I suffered quite a lot of chattering during the race but I could manage."

Lorenzo said to tried and failed to open a gap in the race: "Dani came and he was accelerating and there was much difference on the straights. I tried my maximum but I couldn't follow him."

The hard luck story on Sunday was British rider Cal Crutchlow, whose Yamaha expired on the last lap as he was set to claim third place.

The Grand Prix tour will stop in Malaysia and Australia in the next two weeks with the finale to thrill Spanish fans at Valencia on November 11.