Marquez was the only rider to break the 1'34s barrier with his 1'33.975 while team-mate Dani Pedrosa set a 1'34.124 before crashing with a handful of minutes left on the clock.
But it was bad news for the Monster Yamaha camp as Cal Crtuchlow, who pronounced last night he was 'riding shit', failed to make qualifying two for the first time in this season, edged out by Ducait's Nicky Hayden. Bradley Smith knocked a second off his time from free practice two but still didn't make it through.
Crutchlow will have to fight with Michele Pirro and Smith in qualifying one for a place in final timed session but may be happier for the extra track time to help sort out a setup and confidence that have so far evaded him this weekend.
Jorge Lorenzo yo-yo'd in and out of the pits with a clutch problem but still managed to set the third fastest time - just beaten by Pedrosa late on - with a 1'34.224 while team-mate Valentino Rossi finished in fourth and just a tenth slower.
Andrea Dovizioso, on his home track, stormed into fifth place right at the death with a 1'34.448 to topple old rival Alvaro Bautista while LCR Honda's Stefan Bradl had to settle for seventh.
Andrea Iannone effectively put paid to Crutchlow's entry into qualifying two when he went into eighth place for the session and overall, knocking Nicky Hayden into ninth and Aleix Espargaro makes up the final ten but his time from yesterday puts him ahead of the American in the final analysis.
Danilo Petrucci was the next of the CRT men with Hector Barbera third and 15th overall. Colin Edwards was next along while Michael Laverty seems to have taken a step backwards this morning, finishing 23rd and 3.9s off the pace.