Triple world champion Verstappen retired from a race for the first time in two years after a brake issue in Melbourne caused smoke to billow from his Red Bull.
Carlos Sainz took the chequered flag and team-mate Charles Leclerc followed to claim a one-two finish for Ferrari a fortnight ago.
Verstappen had started the season in typically dominant form, winning emphatically in Bahrain and Saudi Arabia while Ferrari toiled behind.
The tables turned in Australia but the Dutchman has won in Japan for the past two years and Suzuka is one of his favourite circuits.
The sweeping bends and dramatic elevation changes allow Verstappen to make the most of his Red Bull's superior speed, although rain is forecast for Sunday's race.
"We knew a day like this could come at some point," Verstappen said of his premature Melbourne exit.
"So we need to be proud that we have had a great run with nine races (wins) in a row and we can come back stronger for Suzuka."
Verstappen's troubles in Australia compounded a turbulent start to the season for Red Bull, whose grands prix wins were overshadowed by team disunity and allegations against boss Christian Horner.
Verstappen, who said in Australia that he intends to see out his contract with the all-conquering team, will be hoping to find calm at Suzuka.
He has frequently spoken of his love for the "old school" circuit, where he clinched his second world title in 2022 and helped Red Bull seal the constructor's crown last year.
Verstappen romped home by almost 20 seconds from second-placed Lando Norris last year.
This year's race has been shifted forward in the calendar from its traditional late-season slot.
Ferrari resurgent
The reigning world champion could face a stiffer challenge this time round if Sainz's victory in Melbourne is anything to go by.
The Spaniard, who will be replaced at Ferrari by Lewis Hamilton next season, returned from an appendicitis operation that caused him to miss the previous race in Saudi Arabia.
He finished 2.3 seconds ahead of team-mate Leclerc, who now trails Verstappen by only four points in the drivers' standings after three races.
"The team deserves this one-two, we did a fantastic job all weekend," said Sainz, who is fourth overall, 11 points behind Verstappen.
"We executed a perfect race, nailed the strategy and the mechanics were incredible, delivering precise and quick pit stops every single time."
Sainz and Leclerc finished ahead of Norris, whose McLaren team-mate Oscar Piastri was fourth.
McLaren will be looking in Japan to build on that strong showing, especially with once-mighty Mercedes looking a shadow of their former selves early in the season.
Engine failure forced Hamilton out in Melbourne while George Russell escaped a heavy crash on the penultimate lap as the British team failed to finish in the points for the first time in 62 races.
A despondent Hamilton said it was one of his worst starts to a season, with little prospect of better days in the near future.
"It is tough that we are not as competitive as we would like at the moment, but we will keep working hard," said the seven-time world champion.
"In the short term I expect we will still find it difficult to challenge further up, but we will see what we can do in the medium term."
