The WFR Honda rider, who stands third in the points standings, clocked a lap of one minute 37.390 seconds, just under two tenths clear of Michael Laverty.
Championship leader Shane Byrne will be on the second row of the grid after he could only record the seventh best time - having set the pace in Q1 and Q2.
The other title contender, Josh Brookes, is also on the second row of the grid in fifth place.
Race on takes place at 16:00 UK time, live on British Eurosport.
1. Alex LOWES Honda - Team WFR 1:37.390
2. Michael LAVERTY Honda - Samsung Honda 1:37.571
3. Jakub SMRZ Aprilia - Splitlath Redmond 1:37.827
4. Tommy HILL Yamaha - Swan Yamaha 1:37.918
5. Josh BROOKES Suzuki - Tyco Suzuki 1:38.095
6. Luca SCASSA Honda - Padgetts Honda 1:38.191
7. Shane BYRNE Kawasaki - Rapid Solicitors Kawasaki 1:38.346
8. Stuart EASTON Kawasaki - Rapid Solicitors Kawasaki 1:38.448
9. Tommy BRIDEWELL BMW - Supersonic Racing Team GBR 1:38.458
10. Peter HICKMAN BMW - Buildbase BMW Motorrad 1:38.701
British Eurosport is the Home of Bikes, showing all MotoGP, World Superbike and British Superbike races on Sky channels 410 and 411 and Virgin Media channels 521 and 525 as well as eurosportplayer.co.uk
- Josh Brookes