The Brawn GP pair, Renault's Fernando Alonso and Force India's Adrian Sutil failed to slow when yellow flags were waved during the second round of qualifying. Toro Rosso's Sebastian Buemi, whose accident brought out the flags, also drops back five spots.
Button and Barrichello, who had qualified in seventh and fifth places respectively, will now be at a major disadvantage to Red Bull's Sebastian Vettel, who will start from the pole position and still retains slim championship hopes.
"It's disappointing because it's (now) far more difficult to score points tomorrow to try to do what we're trying to do," Brawn GP team principal Ross Brawn said. "It could have been worse. There are examples in the past of far more draconian penalties for doing the same thing. We did commit an offense."
Heikki Kovalainen of McLaren will also drop back five spots for changing his gearbox, while there was doubt over whether Timo Glock of Toyota would be able to take his place in Sunday's race after a heavy crash.
The situation was so confusing that the FIA will wait until Sunday to announce a complete starting grid.
The penalties added a glimmer of hope to Vettel's championship bid. Button leads Barrichello by 15 points. Vettel is another 10 points back in third, with two more races left after the Japan GP.
"Three races to go, it's quite a big gap, but every race has to be a chance," Vettel said. "We are in the best position for tomorrow's race. We have a very, very good chance."
Jarno Trulli of Toyota will start alongside Vettel on the front row, giving the Italian a boost in his effort to attract another team next year. Toyota has gone public with its desire to recruit new drivers.
Lewis Hamilton of McLaren will start from third. The British driver won last weekend's Singapore GP. He has the advantage of the KERS power-boost device and could well be in the lead after the long run down to the first corner.
The penalties came after a number of crashes at Suzuka, the most serious being Glock's head-on collision with a tire wall.
The German was hospitalized with back pain and a cut leg, and Toyota said it will decide early Sunday if he is fit to drive. The team has asked stewards to allow reserve driver Kamui Kobayashi of Japan to step in if Glock can't drive, even though he took no part in qualifying.
Red Bull's chances of catching Brawn GP in the constructor's championship took a hit when Mark Webber damaged his car during a morning crash. He couldn't take part in qualifying and will start from pit lane. Even with Brawn's penalties and Vettel's pole, that will make it difficult for Red Bull, which must score at least seven more points than Brawn on Sunday to retain a mathematical chance in the constructors' race.
Webber crashed into the tire wall at the Degner Curve, and the same long right-hander midway on the lap that later claimed Buemi, Kovalainen and Jaime Alguersuari.
The accidents saw qualifying suspended by red flags three times, disrupting the strategies of all drivers.
Buemi crashed in the closing seconds of the second part of qualifying, causing the incidents that led to the grid penalties. Yellow flags were waved, meaning drivers have to slow in that section. However, both Brawn GP cars, Alonso and Sutil continued at top speed, weaving through the debris.
"I respect their decision, but for me it was the best thing to do," Button said. "I had one second to make a decision."
Buemi was penalized for continuing after hitting a barrier and causing major damage to his car, impeding trailing drivers in the process.