Brookes recorded the fastest time with five minutes remaining of the session on a damp circuit, leading to lap times more than three seconds down on those from FP2.
Friday's front-runner Michael Laverty was second quickest on his Samsung Honda after he and MSS Bathams Kawasaki rider Michael Rutter made a late surge to overtake Noriyuki Haga.
Tommy Hill made it two Swan Yamahas in the top five ahead of Alastair Seeley, Shane Byrne and James Westmoreland with Jon Kirkham and Alex Lowes rounding out the top ten.
FREE PRACTICE SESSION THREE:
1. Josh Brookes AUS Tyco Suzuki GSX-R1000 52.786s
2. Michael Laverty GBR Samsung Honda CBR1000RR 52.835s
3. Michael Rutter GBR MSS Bathams Kawasaki ZX-10R 52.954s
4. Noriyuki Haga JPN Swan Yamaha YZF-R1 53.117s
5. Tommy Hill GBR Swan Yamaha YZF-R1 53.242s
6. Alastair Seeley GBR Tyco Suzuki GSX-R1000 53.254
7. Shane Byrne GBR Rapid PBM Kawasaki ZX-10R 53.391s
8. James Westmoreland GBR WFR Honda CBR1000RR 53.452s
9. Jon Kirkham GBR Samsung Honda CBR1000RR 53.483s
10. Alex Lowes GBR WFR Honda CBR1000RR 53.485s
11. Ian Lowry GBR Padgetts Honda CBR1000RR 53.508s
12. Tommy Bridewell GBR Supersonic BMW S1000RR 53.747s
13. James Hillier GBR Pr1mo BKR Kawasaki ZX-10R 53.796s
14. John Laverty GBR Splitlath Redmond Aprilia RSV4 54.010s
15. Patric Muff SUI Supersonic BMW S1000RR 54.386s