The Honda rider, who started from his ninth pole position of the season, played it safe by avoiding a thrilling tussle between defending champion Jorge Lorenzo and Dani Pedrosa before settling into second place from the 11th lap.
Race officials said they would investigate an incident when Lorenzo appeared to push Pedrosa wide on lap 10, though Marquez's Honda team mate battled back to take second place behind Lorenzo.
Marquez won the title with 334 championship points, four ahead of Lorenzo and 34 in front of Pedrosa.
He passed Freddie Spencer's 30-year-old record from when the American won his maiden crown at the age of 21, also on a Honda, pipping compatriot Kenny Roberts in the final race of the year at Imola in 1983.
"It was the longest race of the year for me," Marquez told Spanish broadcaster Telecinco, with a grin from ear to ear.
"I was very nervous at the start. I know I had said I wasn't, but I was. Jorge started very well and I wasn't sure quite what to do.
"It has been a great year. This has arrived earlier than I expected. Maybe too early, but I want to thank everyone from my team and the fans."
Lorenzo had cranked up the pressure on Marquez by winning the last two races in Australia and Japan, and flew off the grid to hit the front at the first bend with Spanish compatriot Pedrosa in second, and Marquez third.
Pedrosa and Lorenzo went on to delight the fans with a battle for first place with Marquez watching from third, as the two rivals in front of him battled it out, swapping positions over the opening laps.
With 21 laps to go Marquez hit the front, cutting inside the bend as the front two came together and Pedrosa was forced wide, dropping down to fifth.
The 26-year-old Lorenzo muscled his way back to the front a lap later and the title rivals pulled away from the rest of the field, while Pedrosa recovered ground to pressure his Honda team mate in second.
Marquez appeared to let Pedrosa pass him with five laps remaining and cruised across the line, Lorenzo's third successive victory too little, too late.
Marquez went over to where his fans were massed, waving red flags emblazoned with his number 93, climbed on a barrier and threw his gloves into the crowd as he punched the air, and then bowed to them all.
(Writing by Mark Elkington in Madrid, editing by Tony Goodson)
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