Bayliss was injured in the European round at Donington on 1 April

The Ducati rider had most of his right hand little finger amputated after an accident at Donington last time out.

Fellow Australian Josh Brookes took third in a rain-hit Superpole run, with compatriot Troy Corser fourth.

Britain's James Toseland, who leads the championship, could only manage the fifth fastest time on his Honda.

Bayliss said afterwards: "My crash (at Donington) hasn't slowed me down I'm putting it behind me now and moving on.

"I think everyone wants it dry - no-one likes the rain.

"You never feel comfy on the bike and you can't relax especially here at Valencia. My lap was on the limit I just hope everyone else's was."

Leading final Superpole qualifying positions:
1 Troy Bayliss (Aus) Ducati 01min 51.982secs
2 Ruben Xaus (Spa) Ducati 01:52.085
3 Josh Brookes (Aus) Honda 01:52.199
4 Troy Corser (Aus) Yamaha 01:52.733
5 James Toseland (GB) Honda 01:52.801
6 Lorenzo Lanzi (Ita) Ducati 01:52.942
7 Noriyuki Haga (Jpn) Yamaha 01:52.961
8 Yukio Kagayama (Jpn) Suzuki 01:53.634
9 Michel Fabrizio (Ita) Honda 01:53.750
10 Karl Muggeridge (Aus) Honda 01:54.10
11 Giovanni Bussei (Ita) Ducati 01:54.972
12 Max Biaggi (Ita) Suzuki 01:55.196
13 Max Neukirchner (Ger) Suzuki 01:55.965
14 Fonsi Nieto (Spa) Kawasaki 01:56.275
15 Regis Laconi (Fra) Kawasaki 01:56.332