Berikut hasil kualifikasi MotoGP Algarve 2021, Sabtu (6/11).
| POS. | PEMBALAP | TIM | WAKTU/GAP |
| 1 | Francesco Bagnaia | Ducati Team (GP21) | 1'38.725s |
| 2 | Jack Miller | Ducati Team (GP21) | +0.104s |
| 3 | Joan Mir | Suzuki Ecstar (GSX-RR) | +0.168s |
| 4 | Jorge Martin | Pramac Ducati (GP21)* | +0.191s |
| 5 | Johann Zarco | Pramac Ducati (GP21) | +0.193s |
| 6 | Pol Espargaro | Repsol Honda (RC213V) | +0.333s |
| 7 | Fabio Quartararo | Monster Yamaha (YZR-M1) | +0.406s |
| 8 | Alex Marquez | LCR Honda (RC213V) | +0.466s |
| 9 | Franco Morbidelli | Monster Yamaha (YZR-M1) | +0.596s |
| 10 | Iker Lecuona | KTM Tech3 (RC16) | +0.662s |
| 11 | Alex Rins | Suzuki Ecstar (GSX-RR) | +0.924s |
| 12 | Luca Marini | Sky VR46 Avintia Ducati (GP19)* | +1.103s |
| 13 | Enea Bastianini | Avintia Ducati (GP19)* | 1'39.283s |
| 14 | Aleix Espargaro | Aprilia Gresini (RS-GP) | 1'39.389s |
| 15 | Danilo Petrucci | KTM Tech3 (RC16) | 1'39.595s |
| 16 | Valentino Rossi | Petronas Yamaha (YZR-M1) | 1'39.604s |
| 17 | Miguel Oliveira | Red Bull KTM (RC16) | 1'39.624s |
| 18 | Maverick Viñales | Aprilia Gresini (RS-GP) | 1'39.738s |
| 19 | Brad Binder | Red Bull KTM (RC16) | 1'39.859s |
| 20 | Stefan Bradl | Repsol Honda (RC213V) | 1'39.907s |
| 21 | Andrea Dovizioso | Petronas Yamaha (YZR-M1) | 1'39.918s |
| 22 | Takaaki Nakagami | LCR Honda (RC213V) | 1'40.009s |