The drama started in Q1 when Ducati's Francesco Bagnaia crashed heavily while on slicks when the track was still too wet and needed to be taken to the medical centre for checks.
He has been cleared on any fractures for now, but will go to hospital nearby for further examination.
If he is cleared fit to race, he will start from last - a total contrast from November's Algarve GP at Portimao when he was on pole and won the race.
Championship leader Enea Bastianini also crashed and will start 18th, while Suzuki's Alex Rins - second in the championship - will start 23rd after staying out on wets at the end of Q1 when the best laps were on slicks.
In Q2, Zarco snatched pole at the death with a 1m42.003s to beat Suzuki's Joan Mir and Aprilia's Aleix Espargaro.
A late crash for Pol Espargaro at the last corner led to Honda team-mate Marc Marquez having a lap good enough for pole stripped from him as it was set under yellow flags. Marquez was shuffled down to ninth ahead of Espargaro as a result.
Ducati's Jack Miller will start fourth ahead of reigning world champion Fabio Quartararo on the Yamaha, with VR46 Ducati rookie Marco Bezzecchi sixth.
Seventh place went to Q1 pacesetter Alex Marquez, who also crashed at the end of Q2, with Luca Marini eighth on the other VR46 Ducati.
The top 12 was completed by home hero Miguel Oliveira and his KTM team-mate Brad Binder.
2022 MotoGP Portuguese Grand Prix - Full qualifying results
Q2
| Cla | Rider | Laps | Time | Gap | |
|---|---|---|---|---|---|
| 1 |  Johann Zarco |  | 9 | 1'42.003 | |
| 2 |  Joan Mir |  | 9 | 1'42.198 | 0.195 |
| 3 | Aleix Espargaro |  | 9 | 1'42.235 | 0.232 |
| 4 |  Jack Miller |  | 8 | 1'42.503 | 0.500 |
| 5 | Fabio Quartararo |  | 8 | 1'42.716 | 0.713 |
| 6 |  Marco Bezzecchi |  | 9 | 1'42.716 | 0.713 |
| 7 | Alex Marquez |  | 9 | 1'42.903 | 0.900 |
| 8 | Luca Marini | | 9 | 1'43.179 | 1.176 |
| 9 | Marc Marquez |  | 8 | 1'43.575 | 1.572 |
| 10 | Pol Espargaro |  | 7 | 1'43.832 | 1.829 |
| 11 |  Miguel Oliveira |  | 8 | 1'44.066 | 2.063 |
| 12 |  Brad Binder |  | 8 | 1'44.710 | 2.707 |
| View full results | |||||
Q1
| Cla | Rider | Bike | Laps | Time | Gap | |
|---|---|---|---|---|---|---|
| 1 | Alex Marquez |  | Honda | 8 | 1'46.316 | |
| 2 | Luca Marini |  | Ducati | 6 | 1'47.199 | 0.883 |
| 3 | Jorge Martin |  | Ducati | 8 | 1'47.936 | 1.620 |
| 4 | Maverick Viñales |  | Aprilia | 5 | 1'49.332 | 3.016 |
| 5 | Fabio Di Giannantonio |  | Ducati | 6 | 1'49.639 | 3.323 |
| 6 | Andrea Dovizioso |  | Yamaha | 7 | 1'49.695 | 3.379 |
| 7 |  Takaaki Nakagami | | Honda | 7 | 1'49.889 | 3.573 |
| 8 | Enea Bastianini |  | Ducati | 6 | 1'50.618 | 4.302 |
| 9 | Franco Morbidelli |  | Yamaha | 7 | 1'50.702 | 4.386 |
| 10 | Remy Gardner |  | KTM | 4 | 1'50.953 | 4.637 |
| 11 | Lorenzo Savadori |  | Aprilia | 6 | 1'51.308 | 4.992 |
| 12 | Darryn Binder |  | Yamaha | 8 | 1'51.639 | 5.323 |
| 13 | Alex Rins |  | Suzuki | 7 | 1'52.300 | 5.984 |
| 14 | Raúl Fernández | | KTM | 6 | 1'53.603 | 7.287 |
| 15 | Francesco Bagnaia |  | Ducati | 2 | ||
| View full results | ||||||
