Mercedes are back in their usual form after a dismal weekend in Singapore as Nico Rosberg led a team one-two in qualifying for the Japanese Grand Prix.
Hamilton said he might have taken pole had his last lap not been stopped by Daniil Kvyat's crash.
Kvyat rolled his Red Bull and slammed into the barriers after his wheel touched grass.
The driver walked away unscathed.
Williams' Valtteri Bottas and Ferrari's Sebastian Vettel are third and forth behind the Mercedes cars.