Rea was 0.964s off Bautista's pace, having failed to improve on his final run, and his 10th place marks the worst qualifying result of his tenure with Kawasaki.
Having topped the Saturday morning practice after Bautista swept the Friday sessions, Rea took the initial lead with a 1m50.127s, only for Bautista to go a tenth faster right away.
And while the reigning champion shaved off half a tenth from his effort, Bautista immediately responded with a 1m49.798s.
Fellow Ducati rider Eugene Laverty then split he pair, before Tom Sykes lapped just 0.002s slower than Bautista on his BMW.
But Bautista improved once more, holding on to a lead of 0.099s heading into the qualifying-tyre runs in the closing minutes of the session.
Laverty retook second place as he kicked off his final run, and found more laptime on his second attempt, but was left 0.021s adrift of Bautista.
Bautista soon reasserted his dominance, however, as he fired in a brutal 1m49.049s with a minute left on the clock to ensure he would top a second consecutive qualifying session.
GRT Yamaha rookie Sandro Cortese snuck into second place shortly thereafter, lapping 0.365s slower than Bautista, while Sykes denied works Yamaha rider Alex Lowes a spot on the front row by just 0.006s.
Barni Ducati rider Michael Ruben Rinaldi followed Bautista on his fastest lap and took fifth on the grid, ahead of GoEleven rider Laverty.
Sykes' BMW teammate Markus Reiterberger, the second factory Ducati of Chaz Davies and Pedercini Kawasaki rider Jordi Torres will make up the third row of the grid.
Rea's works Kawasaki teammate Leon Haslam will join him on row four, the pair split by the factory Yamaha of Michael van der Mark.
Marco Melandri was eighth when he crashed at the Turn 2 right-hander in the dying minutes of the shoot-out, and was shuffled down to 13th by the time the chequered flag was waved.
Honda's Ryuichi Kiyonari fell at the same spot a minute later, and will star 17th.
|5||21||Michael Ruben Rinaldi||Ducati||6||1'49.689||0.640|
|11||60||Michael van der Mark||Yamaha||7||1'50.264||1.215|