The weather kept the field guessing throughout: heavy rain led to a brief hiatus at the start, while looming clouds appeared with 10 minutes to go, leading many to head back to the pits.
The rain never arrived however and conditions continued to improve right up until the flag, with top spot changing hands on an almost lap-by-lap basis as a result.
Pedrosa, quickest in the opening practice and victor here in the past two seasons, was the man who eventually emerged on top courtesy of a 1m32.228s set two minutes from the finish.
As the flag flew the German fans had the anticipation of seeing LCR Honda's Stefan Bradl go faster in the first two sectors, only for the home favourite to lose time slightly and end the session second fastest, seven hundredths of a second down.
Jorge Lorenzo also set his best time late on, sealing third for Yamaha, while Casey Stoner on the second works Honda ended fourth, having been top with three minutes of the session to run.
Ducati and Tech 3 dictated the next four spots, with Valentino Rossi finishing fifth ahead of Nicky Hayden, Cal Crutchlow and Andrea Dovizioso. All four riders got within 0.6s of Pedrosa's best.
Ben Spies ended the session in ninth on board the second works Yamaha, while Hector Barbera (Pramac Ducati) - quickest with a quarter of the session gone when conditions were at their worst - slipped to 10th ahead of Gresini's Alvaro Bautista.
Following his pitlane crash in practice one, Mattia Pasini managed to get out in the final quarter of the session, ending 14th fastest on his Speed Master machine. Paul Bird's James Ellison set the CRT pace in 12th, 2.6s down on Pedrosa.
Pol Espargaro of Pons 40 HP Tuenti topped both of the Moto2 sessions.
Espargaro, third in the championship, was followed by Technomag-CIP duo Dominique Aegerter and Roberto Rolfo.
Series leader Marc Marquez of CatalunyaCaixa Repsol was down in eighth.
Moto 3 series leader Maverick Vinales topped the second session from fellow FTR Honda rider Jakub Kornfeil, who has led the way in FP1.
Briton Danny Kent was third on the Red Bull KTM Ajo.