Reigning champion Bagnaia of Ducati leads Martin of the satellite team Pramac by 14 points with 37 at stake on the Lusail circuit for this weekend's penultimate race, which may decide the title.
Italy's Luca Marini took his career-second pole position, pulverising the track record with his compatriot Fabio Di Giannantonio and Spain's Alex Marquez second and third.
Spaniard Martin -- who is chasing his first world crown -- has gradually reeled in his Italian rival over the second half of the 20-event season.
Frenchman Johann Zarco of Ducati-Pramac recorded the fastest time in the first qualifying and ended up sixth after round two, taking his place on the second row.
Honda's former champion Marc Marquez hugged Bagnaia's back wheel several times and took seventh place ahead of Maverick Vinales of Aprilia and Raul Fernandez of Aprilia-RNF.
The Federation Internationale de Motocyclisme (FIM) announced that Aleix Espargaro had dropped six places on the grid and received a 10,000 euro ($10,900) fine for hitting Franco Morbidelli's helmet during Saturday's free practice.
In a statement, the FIM said the Spaniard's sanction was due to "aggressive behaviour" and for having hit the Italian.
