The Spaniard finished the 24-lap race in 42 minutes 34.610 seconds, 2.992secs ahead of Andrea Dovizioso and 4.104secs ahead of Maverick Vinales.
His nearest challengers in the title standings, Yamaha pair Valentino Rossi and Jorge Lorenzo, both crashed out.
Honda rider Marquez, 23, is the youngest man to win three premier class world championship titles.
"It was difficult to concentrate [after Rossi and Lorenzo crashed out]," said Marquez. "I am really happy. Really happy with my team."
There are still three races to go this season, starting with next weekend's Australian Grand Prix.
Marquez began the race from second on the grid behind Italian Rossi, with last season's champion Lorenzo also starting on the front row.
It was the latter who seized control in the early stages before Marquez overtook him on the fourth lap.
With 19 laps remaining, Rossi's challenge was ended as he slipped on the tarmac at a hair-pin bend on turn 10.
Lorenzo would follow him out of the race with five laps to go as he also slipped on the track, this time at the V-shaped left-handed turn nine.
This left Marquez to go on and claim the race and the title.
Japan GP results
1.  Marc Marquez (Spain) Honda   42:34.610
2.  Andrea Dovizioso (Italy) Ducati   42:37.602
3.  Maverick Vinales (Spain) Suzuki   42:38.714
4.  Aleix Espargaro (Spain) Suzuki    42:39.336
5.  Cal Crutchlow (Britain) Honda     42:49.659
Championship standings
1.  Marc Marquez (Spain) Honda   273
2.  Valentino Rossi (Italy) Yamaha   196
3.  Jorge Lorenzo (Spain) Yamaha     182
4.  Maverick Vinales (Spain) Suzuki  165
5.  Dani Pedrosa (Spain) Honda       155
Marc Marquez sealed his third MotoGP world championship by winning the Japan Grand Prix on Sunday.