The reigning world champion had control of the pole-deciding Q2 throughout, going fastest by six tenths of a second over Jorge Lorenzo's Yamaha with his first flying lap.
Marquez continued to improve throughout the session to keep the rest of the field at arm's length, despite twice running off track - at the end of the back straight and the first chicane.
The times tumbled throughout the field in the final couple of minutes, with Andrea Dovizioso briefly taking second before he was pushed back by Pol Espargaro with 30 seconds to go.
Friday free practice star Andrea Iannone appeared to have joined in with that scrap when he moved up to P2 inside the final two minutes, but that lap was removed by the organisers due to the Italian taking a short cut on the circuit.
Fourth-placed Stefan Bradl headed the two factory Yamahas of Valentino Rossi and Lorenzo, who were both eight tenths of a second adrift of Marquez's pole time.
There were no celebrations on the other side of the factory Honda garage, as Marquez's team-mate Dani Pedrosa - who recently had 'arm pump' surgery - could manage no better than ninth.
The Spaniard was rooted to the bottom of the top 12 for much of Q2, but he managed to move up a row on the grid in the closing stages.
Aleix Espargaro and Cal Crutchlow got through Q1, although the Brit was given a fright when Nicky Hayden went just 0.036s slower than him towards the end.
1. Jonas Folger (Germany) Kalex 1:37.619
2. Esteve Rabat (Spain) Kalex 1:37.623
3. Luis Salom (Spain) Kalex 1:37.731
4. Mika Kallio (Finland) Kalex 1:37.768
5. Thomas Luethi (Switzerland) Suter 1:37.773
6. Simone Corsi (Italy) Forward KLX 1:37.809
7. Maverick Vinales (Spain) Kalex 1:37.884
8. Ricard Cardus (Spain) Tech 3 1:37.929
9. Sandro Cortese (Germany) Kalex 1:37.963
10. Sam Lowes (Britain) Speed up 1:38.032
- Sports & Recreation
- Jorge Lorenzo
- Andrea Dovizioso
- Andrea Iannone