Verstappen, looking to get back to winning ways this weekend after his first retirement since 2022 in Australia two weeks ago, clocked one minute, 30.056 seconds in the dry opening session to top the times 0.181 ahead of team mate Sergio Perez.
"It was a good start for us... but it does look like everyone is a bit closer compared to last year," said Verstappen, who clocked a record 19 race wins in 2023 including a comfortable victory at Suzuka.
Rain started falling at the figure-of-eight circuit before second practice with teams electing to keep their cars in the garage for much of the session to conserve tyres for the rest of the weekend.
Seven-times world champion Lewis Hamilton, fifth fastest in the first session, ventured out in his Mercedes during a gap between showers but abandoned a flying lap when it started drizzling again.
Japan's Yuki Tsunoda and his RB teammate Daniel Ricciardo offered the fans in the stands some entertainment and recorded the first lap times but they were more than 10 seconds slower than Verstappen's time in first practice.
Australian Oscar Piastri clocked 1:34.725 in a late run on soft tyres in his McLaren, the fastest of the nine drivers who completed flying laps mostly in the last couple of minutes of the session.
Carlos Sainz, who led a Ferrari 1-2 in Melbourne, was third fastest in the opening session 0.213 seconds behind Verstappen, while his team mate Charles Leclerc was sixth, half a second off the pace, behind the Mercedes of George Russell and Hamilton.
The weather made little difference to Sargeant, whose shunt caused a lengthy red-flag stoppage in the opening session and left the Williams mechanics desperately scrambling to get his car ready for Saturday's qualifying.
The 23-year-old American was unable to race in Melbourne two weeks ago after giving up his car to more experienced team mate Alex Albon, who had crashed his own in practice.
Williams patched up the car but arrived in Japan with no spare chassis so Sargeant could miss out again if the team mechanics are unable to repair it in time for Sunday's race.
"Sorry," Sargeant said on the team radio after spinning off at a corner.
The cars return to the track for the third free practice early on Saturday before qualifying in the late afternoon.
