However, because the race was resumed after the red flag, the race counted as full points, and Verstappen now has an unsurmountable lead with 366 points. Perez has 253 and Leclerc 252.
F1 fans were still crunching the numbers and they had their heart in their mouths when Sky Sports presenter Johnny Herbert told Verstappen he had wrapped up the world title in a post-race interview.
Verstappen was unsure if he had in fact sealed the championship, prompting bizarre scenes in the cool down room when he had to clarify what had happened with an official.
He said in the awkward exchange: "But I'm not, no? I am? You sure? Because people keep telling me different."
F1 fans were stunned by the farcical scenes, arguing it was the most underwhelming way possible to crown Verstappen world champion.
The Times' Rebecca Clancy tweeted: "Turns out Verstappen is champion today. Congratulations to him. But total farce today. Bad day for the sport."
F1 broadcaster Jennie Gow said: "So full points were awarded - which means Max is CHAMPION. What a weird set of rules."
"It's crazy," Verstappen later said. "What a year we've had so far, it's been incredible. Something that I could never have imagined after last year. I am so thankful to everyone who has been contributing to this success. To win twice with them is very emotional."
Red Bull Racing team principal Christian Horner said Verstappen continues to improve.
"Winning that first championship last year released a lot of pressure on his shoulders. Carrying that No 1 this year, he has done it with a lot of pride. "We will probably save [celebrations] for after the constructors' championship because that adds so much weight to it as well."
At the start, Verstappen took the lead with a risky pass after a slow start but several cars lost control including Ferrari's Carlos Sainz, who spun and was knocked out. Organisers stopped the race after two laps.
AlphaTaura's Pierre Gasly complained on his radio that he passed a recovery vehicle that was allowed on to the track shortly after the safety car emerged. This incident came just as the race was red flagged.
This is a sensitive issue in Japan. In 2014, French driver Jules Bianchi collided on the course with a recovery vehicle. He was placed in an induced coma and died nine months later.
- With AP