Bautista earned his first MotoGP pole position by edging out American Ben Spies on a Yamaha by 106 thousandths of a second with Australian world champion Casey Stoner taking third at 0.120s.
The 2006 125cc world champion posted a time 0.2s outside the track record set by former MotoGP world champion Jorge Lorenzo in 2010.
Lorenzo came in fourth fastest in qualifying, less than half a second behind his compatriot.
Former multiple champion Valentino Rossi could manage only 10th in the dry conditions.
"I'm so excited. I never thought that I could get a pole position so early (in my career)," Bautista told the BBC. "I felt good on my bike all weekend, both in wet and dry conditions. Morning practice was difficult because rain fell sometimes and then it came again at the end of the qualifying session.
"I'm so happy because my team did a great job. I'm looking forward to tomorrow's race."
British rider Cal Crutchlow is in danger of missing his home race for the second successive year after suffering a heavy crash on his Yamaha in final practice. Crutchlow lost control of his bike at Chapel corner and after landing awkwardly was initially diagnosed with a left-ankle sprain. He was taken to hospital after the ankle swelled up to undergo further tests.
Although he missed qualifying there is still a chance he could start the race from the back of the grid.
Crutchlow was unable to take part in last year's race after crashing in qualifying.
1. Alvaro Bautista (ESP/Honda) 2min 03.303sec, 2. Ben Spies (USA/Yamaha) at 0.106sec, 3. Casey Stoner (AUS/Honda) 0.120, 4. Jorge Lorenzo (ESP/Yamaha) 0.460, 5. Dani Pedrosa (Honda) 0.532, 6. Hector Barbera (ESP/Ducati) 0.573, 7. Nicky Hayden (USA/Ducati) 0.859, 8. Andrea Dovizioso (ITA/Yamaha) 1.001, 9. Stefan Bradl (GER/Honda) 1.732, 10. Valentino Rossi (ITA/Ducati) 2.113, 11. Aleix Espargaro (ESP/Aprilia) 2.980