The 21-year-old Spaniard led from the 11th lap on his Honda and crossed the line in a time of 46 minutes 39.627 seconds, ahead of Valentino Rossi and Dani Pedrosa.
Italian Rossi continued his strong finish to the season and guaranteed himself second place in the drivers' championship after Jorge Lorenzo retired from the race having fallen back to 18th.
Lorenzo decided to change tyres with the threat of rain in the air but the move failed to pay off as there were only a few drops.
Marquez clinched his second successive world title in Japan last month and has now beaten the record for victories in a season which he shared with Australian Mick Doohan who won 12 races in 1997.
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