Marquez, who recently recovered from double surgery on his shoulder and foot last month, had a weekend to remember having also taken pole position and won Saturday's sprint.
The 33-year-old beat KTM's Pedro Acosta to the chequered flag for his first win since the San Marino Grand Prix last year while his Ducati teammate Francesco Bagnaia finished third.
It became a nightmare race for Aprilia when Jorge Martin lost his balance on the first lap at turn one and crashed into three riders, including his teammate and championship leader Marco Bezzecchi.