As conditions remained dry, contrary to forecasts, riders immediately pushed for quick times but found it hard to beat Dani Pedrosa's Friday benchmark.
Jorge Lorenzo got within a few fractions of a second and looked set to end practice three on top.
But in the closing moments, Marquez unleashed a string of ultra-rapid laps on his Honda.
Though the first was stymied by traffic in the final corners, there was no hampering Marquez next time around as he beat his rivals by four tenths of a second.
There was more speed to come, and as the chequered flag fell Marquez put in a 1m33.600s, close to the 2012 pole time, and 0.499s faster than Lorenzo's Yamaha.
Pedrosa was 0.083s down on Lorenzo in third on the second Honda.
Nicky Hayden and Andrea Dovizioso kept Ducati in the hunt in fourth and sixth, split by the unwell Cal Crutchlow's Tech 3 Yamaha.
Valentino Rossi had a quiet morning and was only ninth.
Bradley Smith was another star of the session as he pushed hard to secure a Q2 spot.
Tech 3's rookie was seventh quickest as he managed to move up to 10th on combined times, pushing Aleix Espargaro outside the Q2 cut.
That means the Pramac Ducatis of Andrea Iannone and Michele Pirro will be the only prototypes in Q1.
Alvaro Bautista looked vulnerable to missing the cut when he crashed at the Dunlop chicane and could not get out on his spare bike in time to defend his position.
But with only Smith able to make major gains, the Gresini driver hung on to his Q2 spot.
Bautista's was one of three late falls in the chicane, with Yonny Hernandez and Hector Barbera doing likewise. All three were unhurt.