Brookes lapped in one minute 30.636 seconds at the Leicestershire track, just seven thousandths faster than Alex Lowes.
Michael Laverty was third fastest, 0.147 off the pace.
Lowes had led for the majority of the session until the final three minutes when Brookes his Tyco Suzuki to the top as standings.
Championship leader Tommy Hill was the big disappointment of the day, managing to go only 11th fastest.
The races at Donington mark the final round of the championship before the season-ending showdown, for which Tommy Hill, Josh Brookes, Shane Byrne and Michael Laverty have already qualified.
Donington Park free practice one:
1. Josh Brookes (Tyco Suzuki) 1m:30.636
2. Alex Lowes (WFR Honda) +0.007
3. Michael Laverty (Samsung Honda) +0.145
4. James Westmoreland (WFR Honda) +0.187
5. Luca Scassa (Padgetts Honda) +0.247
6. Alastair Seeley (Tyco Suzuki) +0.256
7. Danny Buchan (MSS Bathams Kawasaki) +0.346
8. Barry Burrell (Buildbase BMW) +0.461
9. Scott Smart (Moto Rapido Ducati) +0.516
10. Jon Kirkham (Samsung Honda) +0.667