"That bike just folded. He was on the brakes and the front wheels just locked."
British MotoGP: Cal Crutchlow crashes in practice at Silverstone
Later in the session, his Ducati team-mate Nicky Hayden went off in exactly the same place when he was on a lap that would have put him on the front row, and will start seventh.
had played havoc on Friday
but, despite dark clouds lingering over Silverstone on Saturday, the rain held off for the start of qualifying.
Yamaha's Lorenzo and Honda's Dani Pedrosa traded fastest laps early on with Pramac's Hector Barbera impressing to run third quickest.
Ben Spies, who finished third fastest in final practice, then eclipsed team-mate Lorenzo's time by 0.3secs with 25 minutes remaining as he looked to put his big crash in last year's race behind him.
Stoner then closed to within 0.014 seconds of the American, before Bautista did what the Australian could and shocked the field with a lightning lap to grab top spot.
Everyone headed back to the pits to prepare for one final run, but with 10 minutes remaining, the rain started to fall, meaning no-one could improve and ensuring Bautista got the first pole position of his career.
“I'm disappointed, to be honest. The bike was a real handful. I couldn't get around there quick at all”
Spies, who scored his first front-row start of the season, said: "It was a good session for us. I set my quickest time on the hard tyre which was surprising. I put the soft tyre on but hit a kerb and wrecked my lap.
"But I'm not complaining. Just being on the front row is good and I hope we can put in a good performance on Sunday."
Reigning world champion Stoner said: "I'm disappointed to be honest. The bike was a real handful. I couldn't get around there quick at all.
"We went in a different direction and the bike felt better so I came straight in for a new rear to go and get pole but the weather pushed it out of our grasp.
"We were confident for pole, it didn't happen, but tomorrow is the important day."
Crutchlow remained in hospital on Saturday afternoon. If the doctors give him the all-clear, he will be able to start Sunday's race, albeit from the back of the grid.
qualified third and fourth in Moto2, while Spain's Pol Espargaro took pole.
Leading positions after Final Qualifying:
1 Alvaro Bautista (Spa) Honda 2:03.303
2 Ben Spies (USA) Yamaha 2:03.409
3 Casey Stoner (Aus) Honda 2:03.423
4 Jorge Lorenzo (Spa) Yamaha 2:03.763
5 Dani Pedrosa (Spa) Honda 2:03.835
6 Hector Barbera (Spa) Ducati 2:03.876
7 Nicky Hayden (USA) Ducati 2:04.162
8 Andrea Dovizioso (Ita) Honda 2:04.304
9 Stefan Bradl (Ger) Honda 2:05.035
10 Valentino Rossi (Ita) Ducati 2:05.416
Leading positions after Moto2 Final Qualifying:
1 Pol Espargaro (Spa) Pons Kalex 2:08.011
2 Andrea Iannone (Ita) FTR 2:08.396,
3 Scott Redding (GB) Kalex 2:08.616
4 Bradley Smith (GB) Tech 3 2:08.844
5 Marc Marquez (Spa) Suter 2:08.864
6 Claudio Corti (Ita) Kalex 2:08.883
7 Thomas Luthi (Swi) Suter 2:09.120
8 Johann Zarco (Fra) Motobi 2:09.353
9 Alex De Angelis (Smr) Suter 2:09.639
10 Simone Corsi (Ita) Ioda 2:09.776
Full information for British MotoGP on BBC TV
Sunday, 17 June
11:05-12:30 - Red Button and Online: Silverstone Moto2
12:30-14:30 - BBC Two + HD and Online: MotoGP: Silverstone. Also commentary on warm-ups and Moto2 from 08:45-12:55 on 5 live sports extra. Race commentary from 13:00-14:00 on BBC Radio 5 live.
14:30-15:30 - Red Button and Online: Silverstone Moto 3
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.