The Spaniard, who lies just 13 points off championship leader Jorge Lorenzo following victories in the last two grands prix, finished almost half a second clear of a field which included the two works Yamahas, LCR Honda's Stefan Bradl and Casey Stoner's injury stand-in Jonathan Rea.
Lorenzo too dipped under the official race lap record on a day in which he also completed more laps on Yamaha's prototype 2013 chassis.
He was unable to match Pedrosa however, finishing 0.488s in arrears. The latter's best effort was more than one second faster than the race record, and almost half a second quicker than team-mate Casey Stoner's pole time from last year.
"In the morning we did some laps to get back into the rhythm and remember the lines on this track, then in the afternoon we really started to work on the bike set up," Pedrosa said.
"We worked a lot with the suspension trying to improve the rear grip especially and with the mapping and electronics to make the bike smoother.
"This is the last test of the season, so it's important to take advantage of it for the upcoming races and see if we can get something else from the bike".
As was the case in testing at Brno last week, Lorenzo said he remained uncertain that the 2013 chassis was preferable to his current frame. He also revealed he would be testing a new M1 engine on Wednesday.
"We're testing the new chassis but there isn't a big difference with the old one," he said.
"With the 1000cc we can beat the 800cc lap record because of the long straight, but we can also be faster in turns.
"Tomorrow we'll keep working with new chassis and maybe with a new engine, which will hopefully be more powerful."
Lorenzo's team-mate Ben Spies, who will leave the works Yamaha squad at the end of the season, ended the opening day in third.
Bradl was fourth ahead of Rea, who ended 2.5s down on team-mate Pedrosa.
"Today I was just getting a good feeling between me and the machine because it still feels very strange," Rea reported.
"I had to work a lot on my brake style today; normally in [WSBK] I don't use so much rear brake but here it seems that I have to learn to use it in every corner!
"Just concentrating on this and getting a better setting on the brakes and trying to do longer runs on the tyres because for me it's very different at the end.
"I feel comfortable on the bike, the riding position is good, but I just need to understand how the traction control is working, what happens when the tyres drop down and be more comfortable with the setup."