Pedrosa from Bradl in wet second session
After a warm and dry morning, a brief but heavy downpour soaked the circuit just before the start of the afternoon 45-minutes.
The deluge soon passed, but the session remained wet thanks to the arrival of further dark clouds and accompanying on-off rain.
But sunshine broke through in the closing minutes, when a dry line also appeared in places and the fastest lap times were set.
Pedrosa - who suffered a big accident while leading the wet 2008 German GP, but has been victorious in the dry for the past two years - led most of the session with his best time coming on the 19th of 21 laps.
Honda LCR rookie Bradl then slotted into second place on his final lap, lapping just 0.076s behind Pedrosa, with joint MotoGP title leader Jorge Lorenzo completing a top three covered by just 0.099s for Yamaha.
Fellow championship leader Casey Stoner was just 0.180s behind his Repsol Honda team-mate Pedrosa in fourth place.
Joining Pedrosa, Stoner, Lorenzo and Hector Barbera in leading the session at some stage was Ducati's Valentino Rossi, who moved from eleventh in the dry to fifth in the wet (+0.304s).
Team-mate Nicky Hayden was a fraction slower in sixth, with Cal Crutchlow recovering from an off-track moment early on reach seventh place for Yamaha Tech 3. Team-mate Andrea Dovizioso was 0.073s behind the Englishman and less than 0.6s from Pedrosa.
Lorenzo's team-mate Ben Spies improved just one place from his tenth in the dry, with Barbera dropping to tenth for Pramac Ducati and Alvaro Bautista eleventh for Gresini Honda.
Bautista will start last on the grid after being penalised for bringing down Lorenzo at turn one in Assen.
PBM's James Ellison used the wet weather to climb from 21st and last this morning to twelfth and top CRT this afternoon, 1.7s from Bautista and 2.6s from Pedrosa.
Mattia Pasini, who was lucky to escape injury when he clipped a Cardion AB team member and fell in pit lane this morning, was back on track and set the 14th best lap time.
Cardion AB's Karel Abraham, who missed the British MotoGP weekend and then withdrew from race day at Assen due to left hand injuries sustained in testing at Aragon, has been replaced by Ducati test rider Franco Battaini this weekend.
39-year-old Battaini, a veteran of the former 250cc class who also spent one season in MotoGP with WCM in 2005, was 19th this afternoon having been 18th in the morning.
Friday practice (2):
1. Dani Pedrosa
2. Stefan Bradl
3. Jorge Lorenzo
4. Casey Stoner
5. Valentino Rossi
6. Nicky Hayden
7. Cal Crutchlow
8. Andrea Dovizioso
9. Ben Spies
10. Hector Barbera
11. Alvaro Bautista
12. James Ellison
13. Aleix Espargaro
14. Mattia Pasini
15. Yonny Hernandez
16. Randy De Puniet
17. Danilo Petrucci
18. Michele Pirro
19. Franco Battaini
20. Ivan Silva
21. Colin Edwards
