The Spaniard, who moved into the championship lead following his third straight podium, led the way with a 1m38.824s set early on in the one-day test.
That was enough to put him narrowly clear of the chasing pack, led by Tech 3 Yamaha's Cal Crutchlow.
Jorge Lorenzo, who has thus far refused to comment on Marquez's last-corner lunge in the grand prix, took third ahead of race winner Dani Pedrosa.
All four men were covered by less than two tenths of a second at the conclusion of running.
Lorenzo's total of 81 laps was comfortably the most any rider managed.
As was the case throughout the weekend, Valentino Rossi trailed his works Yamaha stablemate, his best time more than 0.4s off Lorenzo and 0.5s off Marquez's outright best.
In contrast to the majority of the field though, the Italian set his fastest time in the afternoon running.
Alvaro Bautista put the Gresini Honda sixth ahead of Andrea Dovizioso and Nicky Hayden, both of whom tested the new Ducati chassis Michele Pirro raced with on Sunday.
Neither man found massive improvements, although they were both able to get within nine tenths of Marquez.
LCR Honda's Stefan Bradl and Bradley Smith on the second Tech 3 machine rounded out the top 10 ahead of Avintia's CRT duo Hector Barbera and Hiroshi Aoyama.