The 25-year-old Spaniard led the field home in Friday practice and carried his speed into the qualifying session, setting a time of one minute 56.591 to take his maiden pole of the year.
The track had fully dried in time for qualifying following a wet morning practice and it was reigning champion Jorge Lorenzo and Pedrosa's team-mate Casey Stoner who traded fastest times during the first half of the session.
But Pedrosa responded and his quickest time could not be matched despite Yamaha rider Lorenzo taking four tenths off of his previous best time to secure second place.
Stoner remained third while the second row was filled by Lorenzo's team-mate Ben Spires, Italian Marco Simoncelli of Honda Gresini and Ducati's Valentino Rossi, respectively.
Rizla-Suzuki's wildcard rider John Hopkins did not participate in qualifying after an accident during the wet practice session ruled him of the race weekend. The American crashed at turn three and suffered a dislocation and a fracture to his hand as he slid in the gravel.
Lorenzo www.told motogp.com he was happy to take second on the grid.
"Yesterday (Friday) things weren't like we expected, but we made some changes and improved braking to make the bike more stable," he said
"The lap time improved from that and we got a lot closer to Dani and finished in front of Casey. The pace in the last laps was quite good, so we're happy. Big thanks to my team who worked hard to improve the bike. Tomorrow (Sunday) we aim for the podium or, if possible, to win the race."
American Spies was also content with securing fourth ahead of Sunday's race.
He said: "Today (Saturday), honestly, went a lot better than expected - we're at least in a good starting position for tomorrow (Sunday). I'm not 100% confident about the race and what we can do, but we've shown we've got the speed and the bike is good enough for top five.
"We'll do the best we can, I'm not going to make any promises but I know I've got at least half a good race in me. If we get some good rest tonight then hopefully we'll get lucky and catch a break and be good for it. We're optimistic, the bike is working well and the speed is there, I just hope I can be there too."