The 27-year-old Spaniard, who is set to start his 37th premier class grand prix on Sunday, hit the front with 15 minutes of the hour remaining as his 2m03.303s lap put him a tenth of a second ahead of Yamaha's Ben Spies.
"I never thought that I could get a pole position so early," said a thrilled Bautista, who joined the Gresini team after Italian Marco Simoncelli died in a crash in Malaysia last October.
"But today I felt very good on the bike and in the wet and dry I felt very comfortable. The (qualifying) practice was quite difficult because the rain started sometimes and at the end it started again to rain."
Spies went out to challenge for pole a few minutes later, but was caught out at the Maggotts/Becketts complex as the rain began to fall and ran off the track, ruining his lap.
Despite the track becoming damp several riders, including Casey Stoner and Jorge Lorenzo, went out in search of improvement. Neither managed to move up the order though, allowing Bautista to give the Gresini Honda squad its first pole since last year's Dutch TT.
Spies took a season's best second place for Yamaha with Honda rider Stoner third and world championship leader Lorenzo fourth.
Stoner, who could be making his final MotoGP appearance in Britain if he goes through with his intention to quit at the end of the season, was disappointed with his afternoon.
"We tried a few things at the start and the bike was a real handful to ride and we couldn't get around that quick at all," said the Australian. "So we went another direction and finally found something half-decent.
"The bike felt better so I came straight in to get a new rear (tyre) on and go out and try and get pole but unfortunately the weather pushed it out of our grasp. We were pretty confident of getting pole today."
Dani Pedrosa was fifth for Honda with Pramac Ducati rider Hector Barbera a superb sixth on the best of the Ducatis.
Factory riders Nicky Hayden and Valentino Rossi had near identical crashes at the entrance to Club during the session and could do no better than seventh and 10th. They were split by Tech 3 Yamaha rider Andrea Dovizioso and LCR Honda man Stefan Bradl.
Aleix Espargaro was the best of the CRT riders, the Spaniard putting his Aspar Aprilia 11th, a spot ahead of his team-mate Randy de Puniet.