The Swan Yamaha rider held on to top spot as Samsung Honda's Michael Laverty crashed out in the final minute of the final qualifying session.
“I was pushing hard, made a few mistakes and tried a bit too hard into the corner – it was a silly little crash, losing the front end but I am confident that in the races I can keep the momentum going," said Laverty.
Hill said: “The conditions were tricky and it is always hard to know hard to push on, so I am please to come out on top and now we will have to see how it goes in the races.
"We’ve been going pretty well in the wet as well as this in the dry but the important thing is that we are at the front."
In first qualifying Laverty set the pace ahead of Alex Lowes of WFR Honda.
Reigning champion Hill needed a late charge to take third in that mini-session and progress while Noriyuki Haga crashed out at Clarks but was able to take part in Q2 after Swan Yamaha quickly repaired the bike.
The Japanese, three times a runner-up in World Superbikes, led the way in Q2 from Hill, Laverty and Alastair Seeley of Tyco Suzuki.
In Q3, with Hill having led the way from the initial stages, Laverty made a late bid for pole but crashed at Scotsman. However he will start second on the grid.
Tyco Suzuki's Josh Brookes completes the front row with Shane Byrne (Rapid Solicitors Kawasaki) heading row two from Ian Lowry (Padgetts Honda) and Haga.
“I made little mistakes and they put in impressive lap-times and I am disappointed with myself - but just pleased to be on the front row," said Brookes with regards to the performances of Hill and Laverty.
1. Tommy Hill (Swan Yamaha) 48.785s
2. Michael Laverty (Samsung Honda) +0.068s
3. Josh Brookes (Tyco Suzuki) +0.329s
4. Shane Byrne (Rapid Solicitors Kawasaki) +0.375s
5. Ian Lowry (Padgetts Honda) +0.487s
6. Noriyuki Haga (Swan Yamaha) +0.727s
7. Graeme Gowland (WFR Honda) +0.745s
8. Tommy Bridewell (Supersonic BMW) +0.768s
9. James Westmoreland (WFR Honda) +0.906s
10. Alastair Seeley (Tyco Suzuki) +0.939s