On a wet Friday, George Russell headed Lewis Hamilton to a Mercedes one-two.
Russell was 0.235 seconds quicker than Hamilton and the Red Bulls were third and fourth.
Fernando Alonso, Carlos Sainz and Kevin Magnussen were all in the top five.
There were no lessons to be learned from the wet conditions on the day.
There will be no rain over the weekend.
The F1 race in Japan was not on the calendar for the last two years due to the swine flu.
The Mercedes drivers took a new set of intermediate tires, while Verstappen and Perez did not.
Charles Leclerc, the fastest man over one lap on balance this season, was down in 11th place after complaining of problems with his left front wheel.
If Verstappen wins the race with the fastest lap, he will win the title regardless of the results of Leclerc and Perez.
It would depend on the results of Leclerc and Perez, who are currently 104 and 106 points behind him, with a maximum of 136 still available.
There were no major incidents in the second session after the first ended, after the German lost control after the chequered flag on his return to the pits.
The second session was canceled after Haas decided to change his car's design as a precautionary measure.
Alonso set the pace from the other teams in the first session.