The two Spaniards are effectively the only men in contention for this year's world championship following Casey Stoner's decision to leave Brno and fly home for ankle surgery.
There was little to choose between the pair in the opening practice session of the Czech Grand Prix, although Pedrosa's best of 1m59.003s was ultimately enough to earn him top spot, just over one tenth of a second ahead of Lorenzo.
There was a moment of drama for the Honda man however, as a stone thrown up when Valentino Rossi ran wide and through the dirt hit him on the foot.
He was visibly limping as he headed back into the pits and pulled into his garage, although he was later able to rejoin the track and set his fastest time.
The debris churned up by Rossi's Ducati also caused a brief red flag session to clear the circuit.
When it did resume, the two Tech 3 Yamaha bikes managed to close on the lead pair, with Andrea Dovizioso - who will move to Ducati from 2013 - heading team-mate Cal Crutchlow.
Ben Spies completed a happy session for Yamaha by taking fifth on the second works bike, less than half a second down on Pedrosa.
Gresini Honda's Alvaro Baustita also got within five tenths of the Spaniard, while Valentino Rossi in seventh finished 1.168s down.
LCR Honda rider Stefan Bradl finished eighth, ahead of the CRT duo of Randy de Puniet (Aspar) and Yonny Hernandez (Avintia).
Alongside Stoner, Ducati's Nicky Hayden and Pramac's Hector Barbera will miss this weekend due to injuries suffered at Indianapolis.
Pol Espargaro of Pons 40 HP Tuenti led first practice in the Moto2 class from Tom Luthi and Simone Corsi.
In the opening Moto3 session, Mapfre Aspar Team Moto3’s Jonas Folger set the fastest time ahead of Miguel Oliveira and Sandro Cortese.
- Valentino Rossi
- Casey Stoner