Mercedes' Fin Pilot, Valtteri Bottas, received a 5-place grid penalty for his gearbox change.
Bottas, who completed the first training session on Friday on the dry ground in fifth place, received a 5-line grid penalty for passing the same gearbox to the new gearbox after completing six races.
Bottas also received a 5-place grid penalty at Silverstone this season due to the change of gearbox.
Bottas' championship hopes have also been hit with this punishment coming from Suzuka, where it is difficult to pass. The Finn is now 59 points behind championship leader teammate Lewis Hamilton.
Hamilton, the championship leader, completed his first training session just after Sebastian Vettel from Ferrari. The British pilot finished the second session under the rain in the summit, but Bottas was not on the run.