Dani Pedrosa closed the gap on MotoGP championship leader Jorge Lorenzo to 28 points with a win in Japan.
The pair almost collided going into the first corner as Yamaha rider Lorenzo led from pole position.
But Pedrosa was able to pass his fellow Spaniard on lap 12, and then opened up a comfortable gap to win for the fifth time this season, with Lorenzo second.
Alvaro Bautista saw off a determined challenge from British rider Cal Crutchlow to finish in third place.
The two swapped positions several times in the closing stages before Crutchlow appeared to run out of fuel on the last lap and was forced to retire.
Reigning world champion Casey Stoner was fifth
The in-form Pedrosa has now won four of the last five races looks set to cost him a chance of winning his first championship.
With just three races of the season left, Lorenzo can now afford to finish third in each one and still take the title - even if Pedrosa takes three wins.
And Lorenzo's remarkable consistency - he has finished in the top two of every race apart from Assen, where he crashed out - makes him favourite to regain the title he won in 2010.
Crutchlow said: "All I can do after the way the race finished is take the positives from this weekend and there are a lot.
"There is no denying that I am disappointed as well because I was confident I could have passed Alvaro on the last lap. It wouldn't have been easy because he was riding very well and it was a very enjoyable battle with him.
"I had a lot of fun and I'm sure he did too and it is just unfortunate that we couldn't take the fight right to the very end. Even fourth would have been good for my hopes of finishing fifth in the Championship but I lost a lot of points today.
"We knew fuel consumption was going to be critical. I was very fast and for almost the whole race I was on my own with no slipstream, so I used more fuel.
"I've proven again though that I can fight with the best in the world."
Pedrosa got off to his usual strong start from second on the grid and made a move to pass Lorenzo at turn one, only for the Yamaha rider to cut across and strongly defend his position.
Lorenzo's team-mate Ben Spies then crashed out of third at the start of lap two before the front two pulled out a two-second advantage over Crutchlow.
Stoner briefly threatened to mount a podium challenge but faded as the race drew on.
Crutchlow saved a big slide in the closing stages before Bautista passed him with an aggressive move, only for the Briton to fight back into third spot with three laps left.
The pair touched but Crutchlow's hopes of a second MotoGP podium were dashed on the last lap when he suddenly slowed and had to pull off and retire. He then hitched a lift back to the pits on the back of Lorenzo's bike
There was British success in the day's Moto3 race, as Danny Kent
In the Moto2 race Marc Marquez stalled on the grid as he left his bike in neutral but still made his way through to take victory from Pol Espargaro.
Esteve Rabat was third, with British rider Scott Redding in fourth.
Japanese Grand Prix positions:
1. Dani Pedrosa (Spa) Repsol Honda 42:31.569
2. Jorge Lorenzo (Spa) Yamaha 42:35.844
3. Alvaro Bautista (Spa) Gresini Honda 42:38.321
4. Andrea Dovizioso (Ita) Tech 3 Yamaha 42:47.966
5. Casey Stoner (Aus) Repsol Honda 42:52.135
6. Stefan Bradl (Ger) LCR Honda 42:56.136
7. Valentino Rossi (Ita) Ducati 42:57.641
8. Nicky Hayden (USA) Ducati 43:08.293
9. Katsuyuki Nakasuga (Jpn) YSP Yamaha 43:08.363
10. Hector Barbera (Spa) Pramac Ducati 43:42.298