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The pole-to-flag victory, for the fourth year in a row under the Yas Marina floodlights, left the 26-year-old alone in third place in Formula One's all-time list of winners.
Charles Leclerc finished second after starting on pole position, losing and regaining the lead and then losing it again before passing Sergio Perez on the final lap to deny Red Bull a seventh one-two of the season.
On a nightmare afternoon for Mexican teammate Sergio Perez, who retired after colliding at the first corner with Ferrari's Charles Leclerc, the Dutch 26-year-old also equalled French great Alain Prost's haul of 51 career wins.
Formula One leader Max Verstappen ran away with the Japanese Grand Prix from pole position on Sunday as his dominant Red Bull team secured the constructors' title for the second year in a row. The victory at Suzuka was the Dutch driver's 13th in 16 races this season and left him on the verge of a
McLaren's Lando Norris and Mercedes' Lewis Hamilton completed the top three.
For Red Bull, it was 13th consecutive win, a record in the sport's 73-year history.
The Hungarian GP win was Red Bull's 12th straight.
The Dutch 25-year-old led every lap as he took his career tally to 41 wins, stepping up alongside Brazil's late triple champion Ayrton Senna in the record books.
The win was Verstappen's fourth of the season, second in Monaco and 39th of his career.
Helped by a safety car period that fell in his favour after Verstappen had pitted, the Mexican made the most of his good fortune to take a sixth career victory and become the first driver to win the grand prix for a second time.