Verstappen left his run late, inside the final 10 minutes, to record a soft tyre time that catapulted him to the top of the standings.
He was joined there by team-mate Sergio Perez with the two Mercedes, headed by George Russell third and fourth.
With Fernando Alonso fifth and Lando Norris sixth, Carlos Sainz was the fastest Ferrari driver in seventh, while Charles Leclerc only just scraped into the top 10 – the Ferraris well down on where they were expected to feature.
Oscar Piastri was eighth fastest while Daniel Ricciardo was 13th, just over 0.3s back from team-mate Yuki Tsunoda in ninth.
Conditions had improved from Friday and, while the odd damp patch remained in the cool conditions, the rain stayed away for the start of Free Practice 3.
That tempted Verstappen out of the lane as the session began, the world championship leader heading a host of others that included Perez.
Ricciardo was not initially among them despite having had effectively no running on Friday; he sat out Free Practice 1 and Practice 2 was basically a wash out.
Nor was Logan Sargeant in a rush to get on track following the Practice 1 crash that had ruled him out of the opening day’s latter session.
Having pinched a brake into Turn 3, Kevin Magnussen had a spin at the hairpin inside the opening five minutes.
The Dane wrestled the rear of the car at turn-in, which saw him run out of road and rotate through 180 degrees on the grass verge on the outside of the corner.
Almost 10 minutes had elapsed before Ricciardo trundled down the lane for the first time, a set of soft compound tyres bolted onto his RB.
He was immediately on the pace through the first sector, faster than team-mate Tsunoda and all but matching Perez, who was third best at the time.
Ricciardo ceded much of that by the end of the lap, netting a 1:31.129s on what was effectively his first lap of the weekend, just 0.05s away from his team-mate.
There were some unhappy drivers on track, with Perez complaining about drivability issues and Alex Albon a lack of confidence in his Williams.
After 15 minutes, Lewis Hamilton was the pace setter, his best time a 1:30.065s, just over two tenths faster than what Verstappen managed in Free Practice 3 in Suzuka in 2023.
A mistake from Ricciardo left the Australian pointing the wrong way after he dipped a wheel over the back of the kerb exiting Turn 2.
He went spinning into the grass but, like Magnussen earlier, was able to keep the car running and rejoin with nothing more than a bruised ego.
Having used a set of soft tyres early on, McLaren’s duo of Lando Norris and Piastri sat third and fourth respectively, though Verstappen in second had set his best time on the medium rubber.
Both Ferraris too had only used the yellow-walled rubber, Leclerc sixth and Sainz 10th after 25 minutes of activity.
Tsunoda had risen up the order to sit seventh in the RB, his 1:30.771s just under 0.4s quicker than Ricciardo to that point on what was his second soft tyre run.
A moment for Piastri saw the McLaren driver get up on the kerbs exiting Degner 2 with the tail of the car wagging as he did so.
There was a late change to the order when Russell fitted a set of soft rubber tyres to his Mercedes to shoot to the top of the timesheets.
He sat at the foot of the standings throughout the session, with a strong middle sector being the key to his lap.
The Englishman’s lap signalled the start of happy hour, with Verstappen going fastest on a set of the red-walled rubber by 0.355s.
He was quickly followed by Perez in the other Red Bull Racing, demonstrating the potential in the RB20 this weekend.
Fernando Alonso also improved in what became a frenetic period inside the final 10 minutes that saw him end the session fifth behind the two Red Bull Racings and both Mercedes.
It was an encouraging session for Daniel Ricciardo who desperately needed laps, the Australian logging 23 of them by the chequered flag.
Ferrari, meanwhile, will face a tense debrief, Leclerc especially unhappy with the timing of his final run which saw him caught out by the chequered flag.
In a car considered the second fastest and potentially capable of challenging for pole later today, to languish in 10th is a long way short of expectations.
With practice now complete, teams will turn their attention to qualifying, which begins in Suzuka at 17:00 AEDT.
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