Casey Stoner produced a stunning late lap to take his 10th pole position of the season in Japan.
Jorge Lorenzo looked set to start Sunday's race from the front until Stoner clocked a lap of one minute 45.267 seconds.
Lorenzo will start in second ahead of Stoner's Repsol Honda team-mate Andrea Dovizioso, with Dani Pedrosa in fourth.
Stoner holds a 44-point lead at the top of the standings going into the final four races of the season.
Stoner said: "Everything has gone very well so far this weekend. We've been fastest in all but one session so it's been fantastic.
"Jorge has been riding fantastic, as has Dovi and Dani, but there is no doubt that the Honda suits this track.
"I've been looking forward to riding it here for a while now and I'm not disappointed."
In an event-filled qualifying, Colin Edwards crashed out early on before Marco Simoncelli also fell off going into turn one but was able to dash back to the pits to make it out with 20 minutes of the session left.
Pedrosa led for most of the session ahead of Stoner and Lorenzo.
Stoner went fastest with less than quarter of an hour to go but Lorenzo produced a stunning effort to break the lap record and move to top spot with five minutes left.
However, Stoner was again able to respond and take a quarter of a second out of that time and take another pole.
Valentino Rossi was an improved seventh place, while British rider Cal Crutchlow was down in 12th.
Crutchlow said: "All last night I was coughing and sneezing and I've drank about eight litres of water today and I still feel dehydrated.
"My throat feels like I've swallowed gravel but I still managed to go out there and lap faster than last year's pole time. I can't really ask for much more than that on a circuit I've never even seen before in my life."
Motegi qualifying times:
1) Casey Stoner (Aus) Repsol Honda 1'45.267
2) Jorge Lorenzo (Spa) Yamaha 1'45.523
3) Andrea Dovizioso (Ita) Repsol Honda 1'45.791
4) Dani Pedrosa (Spa) Repsol Honda 1'45.966
5) Ben Spies (USA) Yamaha 1'46.042
6) Marco Simoncelli (Ita) Gresini Honda 1'46.211
7) Valentino Rossi (Ita) Ducati 1'46.467
8) Alvaro Bautista (Spa) Suzuki 1'46.586
9) Hector Barbera (Spa) Aspar Ducati 1'46.694
10) Nicky Hayden (USA) Ducati 1'46.763
12) Cal Crutchlow (GBR) Tech 3 Yamaha 1'46.818