Lowes kept Title Fighter rival Michael Laverty in second as light rainfall hampered the final laps of the session, and his time of 1:37.390 saw him top the sheets.
There was disappointment again for Tyco Suzuki's Alastair Seeley, who dropped outside the top 20, while Ian Lowry didn't make the cut for Q2 for the first time this season.
Lowry dropped out after a final improvement from James Westmoreland saw the WFR Honda rider move through into Q2, while Shane Byrne set the pace from Lowes and Josh Brookes.
Byrne then conquered the second session as he maintained the position at the top of the times for the Rapid Solicitors Kawasaki team, but it was a nerve-wracking final minute for the Samsung Honda and Tyco Suzuki teams as both Laverty and Brookes only moved inside the top 10 on their final flying lap.
In Q3, Lowes headed straight out to set the fastest lap of the weekend ahead of Laverty, while Jakub Smrz scored Splitlath Redmond Racing's first front-row start in third as he edged out Tommy Hill on the leading Swan Yamaha.
Brookes, Scassa and then the two Rapid Solicitors Kawasakis of Byrne and Easton completed row two.
Alex Lowes (WFR Honda) 1:37.390s
Michael Laverty (Samsung Honda) +0.181s
Jakub Smrz (Splitlath Redmond Racing) +0.437s
Tommy Hill (Swan Yamaha) +0.528s
Josh Brookes (Tyco Suzuki) +0.705s
Luca Scassa (Padgetts Honda) +0.801s
Shane Byrne (Rapid Solicitors Kawasaki) +0.956s
Stuart Easton (Rapid Solicitors Kawasaki) +1.058s
Tommy Bridewell (Supersonic BMW) +1.068s
Peter Hickman (Buildbase BMW) +1.311s