The Pramac Ducati rider comes into the Buriram event 27 points adrift of factory Ducati counterpart Francesco Bagnaia after losing the victory in Australia last week on the final lap.
With under half a second covering the top 18, Martin emerged as fastest of all with a final flying effort of 1m29.826s.
However, he did crash seconds later at the Turn 3 right-handed hairpin, but walked away unscathed.
The Aprilia duo of Maverick Vinales and Aleix Espargaro completed the top three, with Australian GP winner Johann Zarco fourth from VR46 pairing Luca Marini and last year’s poleman Marco Bezzecchi.
Bagnaia arrested his recent run of Friday Q2 exits and ended the day seventh, ensuring a direct passage into the pole shootout session in qualifying on Saturday.
The championship leader’s session got off to a rocky start on Friday afternoon as some brake issues forced him to abandon his number one bike early on.
As this was going on, Gresini’s Fabio Di Giannantonio – now favourite to replace Marc Marquez at Honda in 2024 – set the initial pace with a 1m30.945s, before Yamaha’s Fabio Quartararo went top with a 1m30.835s.
Alex Marquez put Gresini back on top moments later with a 1m30.728s, which would stand as the benchmark until Vinales edged clear on his Aprilia with a 1m30.613s 25 minutes into the session.
With just under 13 minutes of the hour-long session to go, the field began switching en masse to the medium rear tyre (the softest option in Michelin’s range in Thailand).
KTM’s Brad Binder breached the top of the timesheets with a 1m30.247s on his fresh medium rear, before improving on his follow-up tour to a 1m30.121s.
Vinales dipped underneath the 1m30s bracket with 10 minutes to go on a 1m29.924s, but it wouldn’t be enough to keep him top of the order.
With two minutes remaining, Martin snatched first away from Vinales with a 1m29.826s, before dumping his Pramac Ducati at Turn 3 as he steamed into the corner a bit too hot.
Trailing the Aprilia duo, Zarco, the VR46 pair and Bagnaia came Quartararo on the Yamaha, with Binder ninth at the chequered flag.
The final direct Q2 spot went to Tech3 GasGas’s Augusto Fernandez, who denied Honda’s Marc Marquez by 0.065s.
Marquez was involved in an odd incident about halfway through the session when he was hit by a winglet broken off of Martin’s bike after he hit a pit-entry marker. Though clearly in some discomfort, Marquez suffered no serious harm.
Franco Morbidelli was unable to join his Yamaha team-mate Quartararo in Q2 in 12th ahead of KTM’s Jack Miller and Di Giannantonio, while Pol Espargaro (Tech3) headed the second factory Honda of Joan Mir in 15th.
Alex Marquez was 18th in the end, but only 0.541s off the pace, highlighting the closeness of the field in Thailand already.
MotoGP Thailand GP – FP2 results