The Red Bull driver converted pole into victory at the Suzuka Circuit, after a lengthy delay following an opening lap crash for Ferrari's Carlos Sainz and heavy rain forcing a restart to be delayed.
The Dutchman was never headed once racing resumed, as title rival Charles Leclerc was demoted to third post-race after cutting the final chicane on the last lap, promoting Verstappen's team-mate Sergio Perez into second and securing the title.
