Racing Kawasaki's Danny Buchan looked set for pole at Brands Hatch before Be Wiser Ducati's Josh Brookes pipped him at the death.
He completed a hat-trick of qualifying crowns on Saturday, winning each session, and it was his 45th career pole courtesy of a 1:25.860 lap.
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Buchan was 0.112 seconds behind him for Racing Kawasaki, and Tyco BMW Motorrad's Christian Iddon took third 0.341 seconds off the lead pace.
Oxford Racing Ducati's Tommy Bridwell claimed fourth, Smiths Racing BMW's Peter Hickman was fifth, and McAMS Yamaha's Jason O'Halloran took sixth to complete the second row.
A technical problem for Scott Redding left the championship leader walking on the grass trying to restart his bike halfway through the session, stuck in ninth place and well off the pace.
Brookes won the second heat with a much improved time from Q1 of 1:26.401. He was followed in second by Buchan, just behind him by two-hundredths of a second.
In third was Brookes' team-mate Redding, with Hickman fourth, Iddon third, and Bridewell in sixth.
Brookes also took pole in Q1.
Teammate Redding was second, with Smiths Racing BMW's Alex Olsen finishing in third.
Brookes scored the fastest lap of the session with a time off 1:27.135, and Redding was a tenth of a second behind.
Olsen secured a time of 1:27.7, with Peter Hickman, Luke Mossey and James Ellison in fourth, fifth and sixth respectively.
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