Fernandez, riding an Aprilia, topped qualifying with a leading lap of one minute and 28.852 seconds in dry and sunny conditions at the Mandalika International Circuit.
The 25-year-old SuperFile-Trackhouse racer was also fastest and set a lap record in Friday's practice.
The Italians Marco Bezzecchi and Fabio Di Giannantonio will join him on the front row.
Championship rivals Marc Marquez and Jorge Martin will line up alongside each other on the second row for Saturday's sprint and the main event on Sunday.
Seven-time reigning world champion Marquez, on a Ducati, was fourth-fastest and 0.266 seconds off Fernandez's pace.
Marquez's fellow Spaniard Martin (Aprilia), who is just two points ahead in the championship standings, qualified fifth.
He was 0.300 seconds off Fernandez, with another Spaniard in Fermin Aldeguer sixth.