Standings leader Brookes (Tyco Suzuki) was unhurt in the crash at Stowe, which occurred 10 minutes from the end of the session. He finished it in fifth.
WFR Honda's Lowes was over two-tenths faster than closest rival Tommy Hill, the defending champion for Swan Yamaha.
His former team-mate Michael Laverty of Samsung Honda was fourth after quick late laps from Hill and Splitlath Redmond Aprilia's Jakub Smrz, who finished third in the list.
The other riders in the Showdown, Shane Byrne and Tommy Bridewell, were seventh and 17th.
1. Alex Lowes (WFR Honda) 2m:07.387s
2. Tommy Hill (Swan Yamaha) +0.227s
3. Jakub Smrz (Splitlath Redmond Aprilia) +0.243s
4. Michael Laverty (Samsung Honda) +0.355s
5. Josh Brookes (Tyco Suzuki) +0.501s
6. James Westmoreland (WFR Honda) +0.550s
7. Shane Byrne (Rapid Solicitors Kawasaki) +0.969s
8. Stuart Easton (Rapid Solicitors Kawasaki) +1.229s
9. Peter Hickman (Buildbase BMW) +1.279s
10. Luca Scassa (Padgetts Honda) +1.314s