In the second period of qualifying for the 2009 Japanese Grand Prix Torro Rosso driver Sebastien Buemi would crash at the exit of the Spoon curve. He would hit the barrier losing his front wing and leaving debris across the track. Yellow flags were shown at this point and several drivers would pass them while on their qualifying runs.

It was later determined that five drivers had not lifted off lifting off during a yellow-flag period. They were Button, Barrichello, Alonso, Sutil and Buemi and as a result they were given five-place grid penalties after the session. The race stewards felt that the first four drivers had not lifted off sufficiently at the point where Buemi had crashed leaving debris on the track.

Buemi was also reprimanded by the stewards for driving back to the pits with a damaged car and impeding other drivers. Button had qualified in seventh, Barrichello fifth, Alonso twelfth, Sutil in fourth and Buemi in tenth. Below is an interim revised grid for the 2009 Japanese Grand Prix. Nico Rosberg was now sixth rather than eleventh.

It was further announced that a definitive grid for the Japanese Grand Prix will be issued prior to the race on Sunday morning. Although a provisional grid had been circulated, a firm decision on the starting order has yet to be made. This was due to the ruling which states that "grid position penalties will be applied to the drivers in question in the order the offences were committed." The final grid will be dependant on the order in which penalties are applied.

Mark Webber and Timo Glock will start from the pitlane having changed chassis after their accidents, while Liuzzi would receive a five-place penalty prior to qualifying due to a gearbox change.