Bradley Perie took pole by more than half a second over Rhys Irwin with a lap of 1min 27.636secs.
Irwin ended the session 0.513s adrift in second position as Jaimie van Sikkelerus stole the final front row spot.
Damon Rees was fourth, just beating Luke Stapleford by 0.122secs.
In the GP2 class, Jack Scott was on top once again in ninth place overall, with Mason Law second and Harvey Claridge third.
Quattro Group British Supersport & British GP2 Cup, Brands Hatch, Qualifying:
1. Bradley Perie (Appleyard Macadam Racing) 1min 27.636s
2. Rhys Irwin (Astro JJR-Triumph) +0.513s
3. Jaimie van Sikkelerus (MPM Routz Racing) +0.727s
4. Damon Rees (Ashcourt Racing) +0.733s
5. Luke Stapleford (Gearlink Kawasaki) +0.855s