Having been fastest at the track all through Friday, the championship contender carried that form into qualifying as he beat VR46 rival Luca Marini to the top spot by 0.138s.
Martin was quick off the blocks in Q2, setting a rapid time of 1m29.491s just five minutes into the session, which was already enough to surpass the previous lap record.
This gave him a 0.167s advantage over Marco Bezzecchi after the first runs, with Brad Binder a strong third on the KTM as the entire field headed back to the pits before the halfway point of the session.
Back on track with fresh tyres, Bezzecchi lowered Martin’s benchmark with a time of 1m29.483s, granting him provisional pole position for the Thai sprint and grand prix.
However, Martin had more time up his sleeve and fought back with a 1m29.287s, which secured him his third consecutive pole position and put him in the prime spot to reduce Francesco Bagnaia’s lead of 27 points in the standings.
Second place on the grid went to Bezzecchi’s team-mate Luca Marini after the Italian made a late improvement to a 1m29.425s on his VR46 Ducati.
Aleix Espargaro was able to repeat the kind of pace Aprilia showed in Friday practice to prevent an all-Ducati front row lock-out, grabbing third late on with a time of 1m29.461s.
This demoted Bezzecchi to fourth in the final order, with Binder likewise dropping to fifth despite finding two tenths on his second run.
Championship leader and factory Ducati rider Bagnaia could only manage sixth, 0.240s down on Martin, after running wide at Turn 1 on his final qualifying attempt.
The Marquez brothers made their way from Q1 to qualify seventh and eighth respectively, with Alex leading the third row on his Gresini Ducati ahead of Honda rider Marc.
Aprilia’s Maverick Vinales, the fastest rider in FP3 earlier on Saturday morning, was a disappointing ninth, albeit only fourth tenths off the pace.
He was followed by Fabio Quartararo on the factory Yamaha, Pramac rider and Australia winner Johann Zarco and Tech3’s Augusto Fernandez.
Fabio di Giannantonio missed out on Q2 progression by 0.002s and will line up 13th on the grid on his Gresini Ducati, ahead of RNF’s Raul Fernandez and KTM rider Jack Miller – who was the most high-profile exit from the first part of qualifying.
Other factory team riders to get eliminated in Q1 were Franco Morbidelli (Yamaha, 18th), Joan Mir (Honda, 19th) and Enea Bastiannini (Ducati, 21st).