The championship leader burst to the front with a 1m38.844s lap in the closing minutes, becoming the first rider to break the 1m39s barrier this weekend.
Until works Honda rider Marquez showed his hand, satellite men Stefan Bradl and Cal Crutchlow had been battling for the top spot for much of the morning.
Bradl ended up second for LCR Honda, with Crutchlow's Tech 3 Yamaha preventing another all-Honda top three by beating Gresini's Alvaro Bautista to third.
Title contenders Dani Pedrosa and Jorge Lorenzo were only fifth and sixth, followed by Valentino Rossi.
Ben Spies is currently undergoing medical chats after a nasty crash. The American was making his comeback this weekend having been sidelined by injuries to his right shoulder for much of the year.
But a crash at Turn 4 resulted in a heavy landing on his other shoulder, leaving the American in clear pain.
His Pramac team-mate Andrea Iannone put in a very strong performance and was on course for Q2 before works Ducati rider Nicky Hayden squeezed him out by 0.017s with a last-minute lap.
Danilo Petrucci pipped Aleix Espargaro to top CRT honours in 12th.