With his previous box having not lasted the required six consecutive events, F1 regulations dictate that Bottas will be penalised at Suzuka, where he finished 10th for Williams last season.
The Finn was fifth fastest in Friday’s opening practice, and did not set a lap time in the washed-out second session.
Team mate Lewis Hamilton, Haas’s Kevin Magnussen and Toro Rosso’s Carlos Sainz – who crashed heavily in FP1 on Friday – have also received new gearboxes, but all without penalty.
Notably, Ferrari’s Sebastian Vettel has not changed gearbox for Japan. There had been fears the German would have to do so following his post-race collision with Williams’ Lance Stroll last weekend in Malaysia.