Simone Corsi claimed ninth place for Ioda Racing, as the highest placed FTR rider, while Andrea Iannone made the top ten for the Speed Master (Speed Up) team in the last qualifying session before he, Marquez and Bradley Smith move to MotoGP.
Still less than a second away from the fastest time were Johann Zarco (JIR Motobi) and Julian Simon (Blusens Avintia) who closed out the session in 11th and 12th places.
Gino Rea will be looking for a repeat of his good form in the wet if the forecast for Sunday rain proves accurate. He finished the session in 20th for Federal Oil Gresini Honda - ahead of fellow Brit Smith who qualified in 22th for Tech3.
Mattia Pasini, who is riding for Forward Racing in place of the injured Alex de Angelis
was 23rd. Axel Pons endured a massive crash near the entrance to pit lane but escaped unharmed after evasive action from the other riders.
Ant West, who is serving a one month ban for his doping result from the Le Mans round, has been replaced at QMMF by Indonesian rookie Rafid Topan Sucipto who qualified in 31st.