Di tempat kedua, Bagnaia menguntir Marquez dengan catatan terbaik 1 menit 34, 250 detik.
Sementara duo rider Mooney Vr46 Racing Team, Bezzecchi dan Marini berturut-turut di posisi ketiga dan empat.
Marco Bezzecchi menorehkan catatan lap terbaik 1 menit 34, 350 detik.
Sedangkan Luca Marini berada satu setrip di belakang eks rider Moto2 itu dengan koleksi waktu terbaik 1 menit 34, 409 detik.
Posisi lima besar ditutup oleh rider Suzuki Ecstar Ale Rins yang mencatatkan waktu 1 menit 34, 633 detik.
Berikut hasil FP3 MotoGP Indonesia 2022.
| POS | RIDER | NAT | TEAM |
| 1 | Marc Marquez | SPA | Repsol Honda (RC213V) |
| 2 | Francesco Bagnaia | ITA | Ducati Lenovo (GP22) |
| 3 | Marco Bezzecchi | ITA | Mooney VR46 Ducati (GP21)* |
| 4 | Luca Marini | ITA | Mooney VR46 Ducati (GP22) |
| 5 | Alex Rins | SPA | Suzuki Ecstar (GSX-RR) |
| 6 | Pol Espargaro | SPA | Repsol Honda (RC213V) |
| 7 | Jack Miller | AUS | Ducati Lenovo (GP22) |
| 8 | Miguel Oliveira | POR | Red Bull KTM (RC16) |
| 9 | Joan Mir | SPA | Suzuki Ecstar (GSX-RR) |
| 10 | Andrea Dovizioso | ITA | WithU RNF Yamaha (YZR-M1) |
| 11 | Franco Morbidelli | ITA | Monster Yamaha (YZR-M1) |
| 12 | Takaaki Nakagami | JPN | LCR Honda (RC213V) |
| 13 | Remy Gardner | AUS | KTM Tech3 (RC16)* |
| 14 | Alex Marquez | SPA | LCR Honda (RC213V) |
| 15 | Maverick Vinales | SPA | Aprilia Factory (RS-GP) |
| 16 | Johann Zarco | FRA | Pramac Ducati (GP22) |
| 17 | Jorge Martin | SPA | Pramac Ducati (GP22) |
| 18 | Fabio Di Giannantonio | ITA | Gresini Ducati (GP21)* |
| 19 | Raul Fernandez | SPA | KTM Tech3 (RC16)* |
| 20 | Brad Binder | RSA | Red Bull KTM (RC16) |
| 21 | Darryn Binder | RSA | WithU RNF Yamaha (YZR-M1)* |
| 22 | Fabio Quartararo | FRA | Monster Yamaha (YZR-M1) |
| 23 | Aleix Espargaro | SPA | Aprilia Factory (RS-GP) |
| 24 | Enea Bastianini | ITA | Gresini Ducati (GP21) |