Marquez started only sixth on the grid at Motegi but scythed his way through the field to claim his eighth victory of the season, passing title rival Andrea Dovizioso with a thrilling move on the 21st of 24 laps to take a lead he never relinquished.
Ducati's Dovizioso, who started from pole and needed to win to keep his slim championship hopes alive, subsequently crashed out on the penultimate lap to leave the way clear for Marquez to take the checkered flag.
Marquez's Repsol Honda teammate Cal Crutchlow of Britain finished second after Dovizioso's late mistake with Alex Rins (Suzuki) edging out MotoGP legend Valentino Rossi (Yamaha) for the final podium spot.
Marquez, still just 25, has now matched the five MotoGP world titles of Australian Mick Doohan and has a total of seven in all classes.
Marquez closing on all-time record
Rossi, who was 26 when he took his fifth, has seven MotoGP crowns, but the last back in 2009.
The record for titles at motorcycling's highest level is the eight 500c championships won by Italian Giacomo Agostini, but the remarkable Marquez is closing fast.
"The big boss will enjoy this," said Marquez after clinching the title at Honda's home track.
"I already imagined it would be decided here but the important thing is that when you have the first chance, you do it."
His victory sparked the usual frenzied scenes in front of a capacity crowd, but there was a bizarre aftermath as a hearty pat on the back from fellow competitor Scott Redding apparently led to Marquez suffering a dislocated shoulder.
He laid down on the track to be briefly assisted by officials before resuming his celebrations.
"The shoulder just popped out. Luckily with the adrenalin it doesn't hurt," he said.
Such is his dominance, Marquez has pulled 102 points clear of Dovizioso with three rounds of the season still remaining.
Rossi, who was involved in a controversial post-race spat with Marquez after the Argentine MotoGP earlier this season, has closed to within nine points of his compatriot Dovisiozo in the standings.
Meanwhile, three-time world champion Jorge Lorenzo, who will join Marquez at Honda next season, has announced he will miss next week's race at Australia after also sitting out the Japanese round due to a wrist injury.
He paid tribute to Marquez on social media: "Sometimes we don't agree the way to compete but I recognize talent and excellence. Congratulations," he tweeted