The new 1000cc bikes were unveiled for the first of three days of testing at a rainy Sepang Circuit in Malaysia, where the riders were returning for the first time since the tragic death of Marco Simoncelli in the Malaysian GP in October.
And it was Yamaha's Lorenzo, who missed the final three races of the 2011 season through injury, who set the quickest time on a good day for the Yamaha bikes, with three of their riders placing in the top five.
Reigning world champion, Stoner, was unable to take part on Day One with a back injury, but the Australian expects to return for Day Two of the test tomorrow.
"I was stretching this morning for a good twenty minutes preparing to go out on track for the first time and then all of a sudden my back just locked up on me, I couldn't move or do anything," Stoner explained.
'I couldn't move or do anything' – Casey Stoner
"I had to call someone to come and help me move into a position that was less painful! Then I had some physio on it straight away trying to get it better for this afternoon but it's wasn't feeling good.
"I had some more physio after lunch but it still wasn't easing up, I felt I could have gone out on the bike in the afternoon but we all agreed it would probably make it worse for tomorrow.
"We have two more days testing here in Sepang, we know the track well and we are getting to know the bike, we just need some time to test the new parts we have here to give feedback to HRC.
"I think tomorrow the track conditions will be better and as long as my back improves overnight we should get back on schedule with our testing programme tomorrow".
But team mate, Pedrosa, enjoyed a productive day and ended the session just 0.346 seconds behind Lorenzo.
"Today was good, for the first laps I think it was important for me to come back and just ride again," Pedrosa said. "Of course, the first day I was a little bit stiff, not totally smooth on the bike, but we completed some laps and they were good.
"Today was mainly a test for myself, to get used to the bike again, recover the feeling, feel the throttle and the brakes after a long time off.
"The whole day I stayed with the same bike that I tested in Valencia in November and tomorrow the real test will start for us, we will work on the set up and probably try a modified chassis that Honda has brought here according to our requests after Valencia".
MotoGP Sepang Test – Day One timings
1. Jorge Lorenzo (Yamaha) 2:01.657
2. Dani Pedrosa (Repsol Honda Team) +0.346
3. Cal Crutchlow (Yamaha) +0.564
4. Ben Spies (Yamaha) +0.577
5. Valentino Rossi (Ducati) +0.735