The triple world champion, who failed to finish the race in Australia a fortnight ago, clocked a lap of 1min 30.056sec — 0.181sec quicker than the Mexican.
Ferrari’s Carlos Sainz, who won in Australia after returning from appendicitis surgery, was third-fastest at 1min 30.269sec.
Verstappen won the first two grands prix of the season but the Dutchman retired from a race for the first time in two years in Melbourne after a brake issue.
Normal service resumed in dry conditions at Suzuka, in a session that was red-flagged for around 10 minutes after Williams driver Logan Sargeant crashed into a wall of tyres.
George Russell was fourth-quickest followed by Mercedes team-mate Lewis Hamilton, with Ferrari’s Charles Leclerc coming home in sixth.
Sargeant came skidding off the track at a corner and spun across the gravel before slamming into a barrier midway through the session.
The American walked away unhurt and his car was carried off by a crane, with the session red-flagged.
Hamilton had the fastest lap at that point but the seven-time world champion soon tumbled down the time sheets once the action resumed.
Hamilton is looking to jump-start a frustrating start to the season after finishing seventh in Bahrain and ninth in Saudi Arabia, before retiring in Australia with engine failure.
Russell, who escaped unscathed from a heavy crash late in the race in Australia, voiced his frustration over the team radio as the traffic piled up.
“This McLaren just stopped in the middle of the corner here,” he said.
McLaren’s Lando Norris, who finished second behind Verstappen at last year’s Japanese Grand Prix, set the early pace.
RB’s Daniel Ricciardo sat out the session as Japanese driver Ayumu Iwasa took his seat for the team.
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