At just 21, Spanish Repsol Honda rider Marquez has back-to-back titles as he built an unassailable lead atop the riders' standings.
Lorenzo (Movistar Yamaha) was a convincing winner in Motegi, but Marquez managed to finish ahead of title rivals Valentino Rossi (Movistar Yamaha) and Dani Pedrosa (Repsol Honda).
That was enough to see him seal the title with three races to spare, having set up his season by winning the opening 10 rounds.
Marquez (312 points) is top of the standings, ahead of Rossi (230), Pedrosa (230) and Lorenzo (227).
Lorenzo rode brilliantly and was in control from early on, eventually cruising to victory by 1.638 seconds.
But all eyes were on an enthralling battle for second between Marquez and Rossi, who could have forced the former to wait to clinch his title.
Marquez made the pass on lap 15 but gave it up almost immediately, only to produce it again before putting space between himself and the Italian.
He celebrated after crossing the line, as did his Repsol Honda team.
Rossi and Pedrosa finished third and fourth respectively, ahead of Ducati pole-sitter Andrea Dovizioso.
Andrea Iannone (Pramac Racing), Stefan Bradl (LCR Honda), Pol Espargaro (Monster Yamaha Tech 3), Bradley Smith (Monster Yamaha Tech 3) and Alvaro Bautista (GO&FUN Honda Gresini) rounded out the top 10.