Byrne's first pole of the season came with a scorching lap which gave him the edge over weekend pace-setter Tommy Hill.
Michael Laverty took third place, while Josh Brookes condemned Noriyuki Haga to the second row in fifth.
"I am always going to be labelled as the Brands Hatch specialist now," Byrne said afterwards, "as it is here I have took the first pole of the season. My crew told me before the session we would need a 1m:25 second lap time and I wasn't sure it would be possible but we are all riding really hard and now we are in a good position for the first race but we need to keep pushing tomorrow."
Hill, who currently leads the championship, remains in a strong position to take the race on.
“It is always good to be on the front row," said Hill, "and that is what you need, especially as it is the same four of us on the front row. We have started the weekend well but it is when the red mist comes down in the other garages you need to be ready and we need to keep making sure we move forwards too."
British Superbike Championship, Brands Hatch GP, qualifying:
Shane Byrne (Rapid Solicitors Kawasaki) 1m:25.908s
Tommy Hill (Swan Yamaha) +0.062s
Michael Laverty (Samsung Honda) +0.297s
Josh Brookes (Tyco Suzuki) +0.431s
Noriyuki Haga (Swan Yamaha) +0.444s
Chris Walker (Pr1mo Bournemouth Kawasaki) +0.448s
James Westmoreland (WFR Honda) +0.505s
Graeme Gowland (WFR Honda) +0.518s
Alex Lowes (WFR Honda) +0.907s
Michael Rutter (MSS Bathams Kawasaki) +0.916s