The Briton was one of five drivers, including Brawn team mate and closest title rival Rubens Barrichello, to be punished for speeding in Saturday's crash-strewn qualifying while yellow warning flags were being waved.
Button can only win the championship on Sunday, with two races to spare, if he scores five points more than Brazilian Barrichello.
That looked unlikely as night fell at Suzuka, with the stewards announcing the starting grid demotions after deliberating for more than three hours.
Button, who needs to finish at least fourth if the title race is not to go on to Brazil in two weeks' time, will now start 12th on the provisional grid with Barrichello ninth.
Red Bull's Sebastien Vettel, the only other contender for the title, will be on pole position alongside Toyota's Italian Jarno Trulli after a chaotic session that had to be stopped three times due to crashes.
Britain's outgoing world champion Lewis Hamilton will line up third with BMW-Sauber's Nick Heidfeld alongside after Force India's Adrian Sutil was dropped five places from fourth.
Renault's double world champion Fernando Alonso, who qualified 12th, and Toro Rosso's Swiss rookie Sebastien Buemi were also handed five place penalties.
Buemi, who scattered debris across the track and brought out the warning flags when he skidded along the barriers in the second part of qualifying, was also reprimanded for impeding others and posing a potential hazard by staying on the track.
The final grid positions were further muddled by uncertainty over Toyota's Timo Glock, who crashed heavily and was taken to hospital.
If he does start, it will be from the pit lane since he will need a new chassis.
A spokeswoman for the International Automobile Federation (FIA) said the grid would not be published before Sunday.
McLaren also changed the gearbox on Heikki Kovalainen's car, dropping the Finn five places from ninth originally. Force India's Tonio Liuzzi, who qualified 19th, also collected a similar penalty but actually moved up to 18th place due to Glock's demotion.
"It was a tough session. No one got any practice yesterday, very little this morning," Button, who is 25 points clear of Vettel with three races remaining, told the BBC.
"Three red flags is very unusual so I hope everyone is OK. I think we've got a reasonable amount of fuel on board ... I'm not looking at Sebastian really."
All of the top three drivers had team mates who crashed, with Glock's accident the most serious. The German plunged into the barriers at the final corner only hours after he had been passed fit to race.
The German, who missed Friday's rain-hit practice because he had a heavy cold and fever, waved and gave a thumbs-up sign as he was extracted from the car but was then flown on to hospital for further checks.
A team spokesman said he had a shallow 5cm cut to his left leg and back pains. Vettel's Australian team mate Mark Webber did not take part in qualifying and will also start from the pit lane after damaging his car in a crash in final practice.
Kovalainen, one of several drivers without previous experience of a challenging circuit making its return to the calendar for the first time since 2006, went into the tyre wall at the Degner curve in the final phase of qualifying.
Toro Rosso's Spanish rookie Jaime Alguersuari brought out the first of two red flags in the space of 11 minutes when he ploughed into the tyre wall in the second phase. He was unhurt.
Vettel's pole was his fourth of the year and he needs to take his third win of the season to stay in genuine contention.
Red Bull must also score seven points more than Brawn on Sunday to prevent that team from taking the constructors' championship.
