The Red Bull driver dominated a time-limited and controversial event at Suzuka to win by close to half a minute, but not scoring the bonus point for fastest lap looked to leave him one point short of the title.
However, a post-race 5s penalty for runner-up Leclerc - adjudged to have gained an advantage by running through the last chicane - dropped the Ferrari racer behind the Mexican to hand Verstappen the championship.
The ever-changing weather forecast for the Suzuka weekend culminated in the rain shower that was originally predicted to hit after the race instead dousing the grid in the build up.
As such, all drivers opted for intermediate tyres for what was kept as a proper standing start.
But conditions proved marginal, as the red flag was deployed owing to a messy opening lap.
Leclerc had enjoyed the superior launch, despite the limited grip, to draw alongside polesitter Verstappen and the Ferrari even pulled ahead by half a car length. However, the Red Bull driver kept his foot in through the first corner to hold the line and decisively retake first place.
Vettel took sixth, having gained a position after Alonso made a late stop for inters to fall to 10th before climbing back up the order, as behind the Alpine ranked George Russell.
The Mercedes was one of few climbers but neatly passed Yuki Tsunoda, Norris and Latifi for ninth.
Latifi’s early move for inters returned points in ninth place as Norris completed the top 10 over team-mate Daniel Ricciardo.
