Pedrosa, who completed a clean sweep of the first test, edged out 2012 champion Jorge Lorenzo by just over two tenths of a second.
Both men set their best times in the early part of the day, before the onset of rain effectively washed out the afternoon.
Marc Marquez continued his own impressive build-up to what will be his rookie season, finishing third fastest and getting to within four tenths of Pedrosa's time.
He was just 0.017 seconds quicker than Stefan Bradl, the man who beat him to the 2011 Moto2 crown.
Bradl, riding as a Honda factory supported rider this year, was in turn only 0.069s than Valentino Rossi on the second Yamaha.
After a poor start to the year and calls for major changes, Ducati's works team fared better in the second test as Andrea Dovizioso and Nicky Hayden locked out eighth and ninth.
That put them behind Tech 3's Cal Crutchlow and Gresini's Alvaro Bautista, but within 1.5s of the outright pace.
Pramac satellite riders Ben Spies and Andrea Iannone were however outpaced by the fastest of the CRT riders, Aspar's Aleix Espargaro.
The test attracted a 27-bike field, with the 2013 entrants once again bolstered by Yamaha test duo Katsuyuki Nakasuga and Wataru Yoshikawa. Honda's counterpart Takumi Takahashi and Ducati's Michele Pirro were also present.
Paul Bird's Michael Laverty was unable to get out however as the team spent much of the day putting the finishing touches to the in-house chassis it will run for the Northern Irishman this year.
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- Stefan Bradl