The Spanish Repsol Honda rider has been in impressive form since returning from his collarbone injuries, and set a best time of one minute 50.281 seconds at the Motorland Aragon circuit during the first practice session.
He was denied the chance to improve that time in the afternoon as a series of power cuts first forced organisers to delay the session before a decision was made to cancel it, with an extended final practice session set for Saturday morning instead.
Pedrosa's excellent lap left him almost half a second clear of reigning world champion Jorge Lorenzo, the Yamaha rider having led the times until Pedrosa responded in the final five minutes.
Pedrosa's team-mate and current championship leader Casey Stoner was back in third, having initially set the pace in the blazing sunshine, while Marco Simoncelli made it three Hondas inside the top four on his San Carlo Gresini machine.
The third Repsol bike of Andrea Dovizioso was fifth while Randy de Puniet produced arguably the performance of the day as he took the tag of top Ducati on his Pramac bike.
Nicky Hayden and Valentino Rossi were next up on the factory Ducatis, and it proved to be a particularly difficult day for the Italian.
Rossi was trying out a new aluminium chassis as the Italian marque continue to try and make up their shortfall in pace to Honda and Yamaha. But the nine-time world champion took two trips through the gravel before eventually ending the day eighth.
Colin Edwards was a solid ninth on the Tech 3 Yamaha but team-mate Cal Crutchlow was back in 14th place.
Pedrosa said: "In the morning session we were basically trying to get the feeling from the race track and we started well, the bike was working okay.
"We saw that the softer compound of tyre is maybe too soft, so not really the one for the race if the high temperatures remain, so we also tried the medium compound and I felt comfortable.
"In the afternoon the practice was cancelled which is a shame as the weather conditions were perfect.
"Of course we will have a longer session tomorrow [Saturday] morning but you cannot take the same benefit from it.
"With two sessions of 45 minutes you have time to analyse the data and make the changes you need for the second practice, while in 1hr15m you cannot. Anyway, it's the same for everyone, so let's hope everything is okay tomorrow [Saturday] and we can keep improving the bike and have a good qualifying."