Today’s final practice was cancelled and qualifying shifted to tomorrow morning.
Yesterday’s afternoon session at the Suzuka circuit will decide the starting grid for the race if conditions have not improved enough for the hour-long qualifying at 10am (4am Bahrain time) tomorrow.
“(I’m) really happy with the car in general,” said Bottas who lapped the 5.8km track in one minute, 27.785 seconds to beat championship leader Hamilton by 0.100.
“Just still minor things with the balance to tweak but both short and long runs at least today (were) good,” added the Finn who also led his five-time champion team mate in the first session.
Mercedes, who have won every race at Suzuka going back to 2014, can seal a record-equalling sixth successive Formula One constructors’ championship tomorrow by scoring 14 more points than Ferrari.
Hamilton, 73 points clear of Bottas in the overall standings with five races to go, is also well on his way to clinching a sixth title even if he cannot get the job done in Japan.
“It’s a work in progress,” said the Briton. “When you first get on the track you’re pushing the limits, there’s always time to find at this track. This is not, I would say, my strongest circuit.
“There’s always areas you can improve,” added the 34-year-old who has won four times at Suzuka and five in Japan overall, just one short of Michael Schumacher’s record haul of six Japanese Grand Prix wins.
Given the second session’s potential to decide the grid order, it assumed greater importance than usual.
Max Verstappen went third fastest for Honda-powered Red Bull, making a strong start to the Japanese engine supplier’s home weekend.
The Dutchman had been fourth in the morning but vaulted past Charles Leclerc and Sebastian Vettel in the afternoon to push the Ferrari pair down to fourth and fifth.
Ferrari have been the team to beat since Formula One’s August break, starting the last four races from pole and converting three of those to victory.
But they appeared to have fallen back slightly after their recent resurgence.
“We made the most out of our day, which was the most important, but it seems we are lacking pace this weekend,” said Leclerc, 21.
Alexander Albon was sixth for Red Bull ahead of McLaren’s Carlos Sainz and Racing Point’s Sergio Perez.
Frenchman Pierre Gasly, who gave up his seat in the opening session so Naoki Yamamoto could drive his Honda-powered Toro Rosso in front of his home crowd, was ninth with McLaren’s British rookie Lando Norris 10th.