Marquez's pole lap was a spectacular effort, which saw him arrive at the final chicane sliding slightly sideways as he dived down the outside of the slower-moving Simone Corsi and still come through to beat his rivals by nearly half a second.
The Spaniard then had a high-side at Turn 5 on his next run, but was unhurt - despite a heavy landing - and able to right his bike and return to the pits.
Title contender Pol Espargaro (Pons) was on top until the Monlau rider deposed him five minutes from the end, leaving Espargaro to hang on for second.
Andrea Iannone completed the front row for Speed Master.
It was a good day for some of Moto2's Swiss contingent, as Team Switzerland's Randy Krummenacher achieved his best Moto2 grid spot yet in fourth, just ahead of compatriot Dominique Aegerter (Technomag-CIP), who equalled his Moto2 career best. But Switzerland's title protagonist Thomas Luthi was only 10th on the Paddock Suter.
Corsi (Ioda) qualified sixth, ahead of British duo Scott Redding (Marc VDS) and Bradley Smith (Tech 3), with Alex de Angelis's Forward FTR next up.
The session also saw crashes for Italtrans' Claudio Corti, QMMF duo Anthony West and Elena Rosell, and JIR's Johann Zarco. All escaped injury.