On a day when world champion Casey Stoner was injured, Pedrosa used a soft compound Michelin to set a 1min 39.993secs - half a second off his own pole position time from the Spanish Grand Prix in March - on his final lap of the day.
That placed the Repsol Honda rider just 0.141secs in front of Yamaha's Valentino Rossi, but Rossi - like the rest of the Wednesday top five - also set his best time with a qualifier, prior to which Pedrosa had been quickest on race rubber.
"We ended up with the fastest time of the day which is nice, and the day's testing was pretty productive," began Dani. "We started quite late again this morning after waiting for the track conditions to warm up and we also spent quite a lot of time stopped in the garage making machine setting changes, but this is normal for testing. In the afternoon we did more laps, making further set-up adjustments and continuing the work from yesterday.
"We've been doing short runs of not many laps because it's a new bike and there are many small things to adjust. When we have done this base work we will begin to do longer runs. My fastest lap today was on qualifying tyres because it's important to see how the bike reacts with the extra grip.
"It was not a bad lap time, especially since it's the first time with this bike on qualifiers at Jerez, though we're not at the level that we were at the end of the season when I took the four pole positions in a row. We didn't have time to test the other Michelin tyre options here today so there's plenty of work still to do tomorrow,2 he concluded.
Team-mate Nicky Hayden was sixth fastest after electing not to run a qualifying tyre. Hayden's quickest lap of 1min 40.692secs was an improvement of 0.3secs over day one and the 26-year-old American was only 0.04secs behind Pedrosa's best on race rubber.
"I think we picked up where we left off yesterday and the test went quite well again," said the 2006 world champion. "We didn't work any miracles out there but we chipped away at the times and made some improvements. I wasn't a lot faster today but I was able to take a little bit off the lap time and was certainly more consistent in my pace than before.
"I think everyone in front of me today used qualifying tyres and as far as the team knew nobody went faster than 1min 40.6secs on race tyres, which is pretty encouraging because yesterday I was definitely off by a couple of tenths on race tyres.
"Today we were right in there, the team's done a good job and we had quite a good day. We were trying some quite big changes with the chassis set-up today which is what you have to do to learn how the bike reacts and behaves in different conditions. Overall we collected a lot of useful information and hopefully we can keep the progress going tomorrow," he added.
2007 MotoGP testing concludes at Jerez on Thursday.