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.
The Spaniard, yet to win in 2012, said he could not afford to relax despite his pace in both the dry and wet on the opening day.
"The weekend has started pretty good for us; I felt comfortable in both the dry and wet conditions, but we cannot relax," Pedrosa said.
"The times are very close here, as usual, and we still have margin to improve."
Pedrosa admitted the afternoon rain had interrupted Honda's practice programme, but said it could also prove useful given the unstable conditions forecast for the remainder of the weekend.
"We only managed half of our plan today," he admitted.
"We wanted to test the hard rear tyres in the afternoon, because in theory the hardest compound should be working better in this track where you are leaning to the left a long time, and with the soft the bike slides a lot.
"Anyway, it's been also good to try the bike in the wet for one practice session because it looks like the weather will again be very unstable.
"Today I've been using the new chassis we received in Assen and the feeling was OK, but weather permitting, I would like to compare both chassis again tomorrow before qualifying."
Team-mate Casey Stoner meanwhile said he was happy with his pace in the both wet and dry conditions, but did highlight an issue with rear chatter.
"We were pretty happy in both conditions today. In the dry we felt comfortable and we had a consistently higher pace than the others, and we're confident we can go quite a bit faster," he said.
"We were struggling a little at the beginning in the wet, we needed to find more rear traction but the conditions weren't perfect as they were changing throughout the session with some parts of the track drying out and then more rain arriving.
"Unfortunately we have some bad chatter in the rear, especially on the right hand corners, both in the wet and dry so we need to improve this before the race."
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 Stoner on the second works Honda ended fourth, having been top with three minutes of the session to run.
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.