Max Biaggi, fastest in Friday qualifying and Saturday free practice at Valencia, will start from just 18th on the grid after being eliminated in the very first phase of Saturday's knockout Superpole session.
The lone Aprilia rider, following a shoulder injury for team-mate Shinya Nakano, had been expected to battle the likes of Ben Spies and Noriyuki Haga for pole but instead failed to graduate through the first of the three 12-minute sessions.
Yamaha's Tom Sykes and BMW Ruben Xaus joined Biaggi on the sidelines, with the injured Nakano not registering a lap.
At the sharp end, the session was led by Carlos Checa, who set the fastest lap of the weekend so far - a 1min 34.119secs - to head Sterilgarda Ducati's Shane Byrne and Suzuki Alstare's Yukio Kagayama.
John Hopkins, making his WSBK debut at Valencia, made it safely through Superpole 1.
Grid positions nine to 16 will now be decided in Superpole 2, with the top eight riders in that session then graduating through to Superpole 3.