The Repsol Honda rider - already guaranteed the title - enhanced his MotoGP standing further on Saturday by becoming the first rider to secure 13 poles in a single season at the Sepang International Circuit.
And the weekend continued in a similar vein as Marquez drew level with the mark set by Australia's five-time world champion Doohan by finishing clear of Valentino Rossi and Jorge Lorenzo.
The victory was Marquez's first since his triumph at Silverstone in August, while Rossi and Lorenzo will battle it out for second place in the final race of the season in Valencia after Dani Pedrosa crashed out.
Despite veering into the gravel, Marquez was quickest in the warm-up at Sepang but it was Pedrosa and Lorenzo who made strong starts.
Marquez slipped to sixth after running wide as Lorenzo surged into the lead before a series of riders saw their races come to a premature end - Aleix Espargaro and Alvaro Bautista forced out after a crash at turn one.
A mechanial fault signalled the end of Cal Crutchlow's race and Pedrosa then retired as he crashed for a second time, having recovered to 11th following a failed bid to challenge Lorenzo at turn 15.
At the front, Rossi threatened to make it back-to-back victories as he led Lorenzo and Marquez but the two-time world champion recovered to claim top spot by 2.445 seconds.
Lorenzo was 3.508secs further back, and Marquez could now cap a memorable season in Valencia - a win in his homeland would take him past Doohan's record.
Just 12 points seprarate Rossi and Lorenzo, with the battle for second going down to the wire.
Marquez's victory also helps ensure Repsol Honda of a 63rd Constuctors Championship across all classes - their 21st in the premier class and eighth in MotoGP.