Verstappen, who failed to finish the race in Australia a fortnight ago, blazed round the Suzuka track in dry conditions in 1min 29.563sec - 0.269sec quicker than Perez.
All the drivers went out after showers spoiled Friday's second practice and saw just five record timed laps.
George Russell was third-fastest with a time of 1min 29.918, ahead of Mercedes team-mate Lewis Hamilton.
Aston Martin's Fernando Alonso was fifth and McLaren's Lando Norris - second in last year's race behind Verstappen - was sixth.
Carlos Sainz, who won in Melbourne, was seventh in his Ferrari.
Verstappen won the first two grands prix of this season but he retired in Melbourne after a brake issue.
He did not emerge for the wet second practice at Suzuka on Friday, but he was first out on the track for the final session in better weather.
Haas's Kevin Magnussen skidded off early on before resuming his lap.
RB's Daniel Ricciardo also suffered a setback when he misjudged a corner and spun onto the grass.
Williams driver Logan Sargeant was back in action after crashing in Friday's first practice and sitting out the second session.
But the American was still not happy, telling his team over the radio that he had "no rear support, zero".
