Jorge Lorenzo kept his cool to ride to pole for tomrrow's Jerez Grand Prix as his title rivals buckled under pressure as they tried to close the gap to him.
Pedrosa and Rossi crashed within seconds of each other towards the end of the session, leaving them unable to make full advantage of qualifying tyres.
Pedrosa managed to hold second, ahead of teammate Marquez, continuing to impress on his debut season.
Cal Crutchlow, fastest in this morning's free practice, was fourth, after crashing earlier in the session but managing to make it back out on his second bike. His heavy crash saw him hit the gravel and cartwheel multiple times, although it appeared to not slow his pace.
Rossi was fifth on the second of the factory Yamahas, although he managed to destroy bike in his crash.
Bautista was sixth on his Honda, while Nicky Hayden was best of the Ducatis in seventh. Stefan Bradl was eighth, having to come through from Q1 after a slow start to the weekend.
Dovizioso on the second factory Ducati was ninth and Hector Barbera was the first of the CRTs in tenth, the only CRT machine to make it through to Q2.
Bradley Smith was twelth, like Bradl, a refugee from the earlier Q1 session. Michael Laverty was 22nd, ahead of only Lukas Pesek.
Karel Abraham will not race, after determining this morning that he's still suffering from too much pain in the collarbone he broke at Austin.
Birthday boy Lorenzo said "Its a good present to get this pole position. I knew track conditions were not good because of all the crashes in other classes. I didn't get a perfect lap, because I made some braking mistakes, but I made a good one. Tomorrow I think the conditions will be much slower, so nwo we have to adjust the bike for that."
1 99 Jorge LORENZO 1'38.673 Yamaha
2 26 Dani PEDROSA 1'38.920 Honda
3 93 Marc MARQUEZ 1'38.971 Honda
4 35 Cal CRUTCHLOW 1'39.262 Yamaha
5 46 Valentino ROSSI 1'39.300 Yamaha
6 19 Alvaro BAUTISTA 1'39.509 Honda
7 69 Nicky HAYDEN 1'39.654 Ducati
8 6 Stefan BRADL 1'39.847 Honda
9 4 Andrea DOVIZIOSO 1'39.848 Ducati
10 8 Hector BARBERA 1'39.980 FTR
11 29 Andrea IANNONE 1'40.087 Ducati
12 38 Bradley SMITH 1'40.356 Yamaha
13 41 Aleix ESPARGARO 1'40.085 ART
14 51 Michele PIRRO 1'40.182 Ducati
15 14 Randy DE PUNIET 1'40.466 ART
16 7 Hiroshi AOYAMA 1'40.654 FTR
17 9 Danilo PETRUCCI 1'40.852 Ioda-Suter
18 67 Bryan STARING 1'41.324 FTR Honda
19 71 Claudio CORTI 1'41.513 FTR Kawasaki
20 5 Colin EDWARDS 1'41.536 FTR Kawasaki
21 68 Yonny HERNANDEZ 1'41.779 ART
22 70 Michael LAVERTY 1'41.935 PBM
23 52 Lukas PESEK 1'43.220 Ioda-Suter