The Honda rider, who is pulling double duty after stepping in to replace the injured Casey Stoner in MotoGP, set the best time at one minute and 55.157 seconds on the arduous 5.137km-lap course in Germany.
Marco Melandri of BMW Motorrad showed a vast improvement to finish with the second-fastest time of 1’55.182, a quarter of a second behind the Northern Irishman with his main championship rival Max Biaggi (Aprilla) third.
Kawasaki’s Tom Sykes, also in contention, came fifth behind Ducati rider Carlos Checa.
The competitors have a final free practice coming up on Saturday lunchtime before the three Superpole events later in the day.
The main race and warm-up take place on Sunday.
QUALIFYING TWO - TIMES
1. Jonathan Rea (Honda World Superbike Team) Honda CBR1000RR 1'55.157
2. Marco Melandri (BMW Motorrad Motorsport) BMW S1000 RR 1'55.182
3. Max Biaggi (Aprilia Racing Team) Aprilia RSV4 Factory 1'55.249
4. Carlos Checa (Althea Racing) Ducati 1098R 1'55.270
5. Tom Sykes (Kawasaki Racing Team) Kawasaki ZX-10R 1'55.325
6. Davide Giugliano (Althea Racing) Ducati 1098R 1'55.385
7. Leon Haslam (BMW Motorrad Motorsport) BMW S1000 RR 1'55.541
8. Leon Camier (FIXI Crescent Suzuki) Suzuki GSX-R1000 1'55.594
9. Chaz Davies (ParkinGO MTC Racing) Aprilia RSV4 Factory 1'55.703
10. Eugene Laverty (Aprilia Racing Team) Aprilia RSV4 Factory 1'55.783