With two further sessions of running in the Moto2 and Moto3 classes ahead of MotoGP FP2, the track was a bit cleaner than it was this morning and lap time gains were instant.
Pramac’s Johann Zarco set the early pace with a 1m33.310s, which was just over a tenth quicker than Pol Espargaro’s FP1 best.
At around the same time, there was an issue for fellow Frenchman Quartararo as his factory Yamaha cut out at Turn 5.
This served to compound what had already been a tough day for Quartararo, who struggled in 16th in FP1.
Losing 10 minutes while he made his way back to the Yamaha garage for his second bike, Quartararo returned to the circuit on a used soft rear and began to put in some quick lap.
Jumping up to fourth, Quartararo would eventually find his way to the top of the timesheets with a 1m32.570s, taking over from KTM’s Miguel Oliveira.
With weather forecasts uncertain for Saturday, a salvo of flying laps at the end of the session came in at the end of FP2 as the field made their bids for a provisional top 10 to get into Q2 in qualifying.
Top spot changed hands several times, as both Pramac Ducati riders took turns leading the session towards the end.
But it was Quartararo who emerged fastest of all with a 1m31.608s to pip Yamaha teammate Franco Morbidelli by 0.030s.
Johann Zarco completed the top three on his 2022-spec Pramac Ducati, with Qatar poleman Jorge Martin trailing him by 0.011sn fourth.
Qatar race winner Enea Bastianini leaped up to fifth late on just before he crashed his Gresini Ducati, with Jack Miller on his factory team GP22 sixth.
Aleix Espargaro was seventh on his Aprilia ahead of factory KTM duo Brad Binder and Oliveira, while Suzuki’s Alex Rins sneaked into 10th at the death with a 1m32.106s.
Six-time MotoGP world champion Marquez was left stranded in 22nd on the combined order after suffering a fast front-end crash at the Turn 11 right-hander as he pushed for a lap time.
This, coupled with Bastianini’s crash, led to yellow flags being waved, which seemed caught out by several big hitters.
Suzuki’s Joan Mir was only 20th ahead of Ducati’s Francesco Bagnaia, while FP1 pacesetter Pol Espargaro on the second factory team Honda was 19th.
Practice for the Indonesian Grand Prix continues on Saturday morning with FP3 at 10:50am local time (2:50am GMT).