The latter, currently 18 points clear of Pedrosa in the championship, had been looking comfortable at the top of the timesheets for much of the session, but 17 minutes from the flag he lost the front of his Yamaha in the Stadium section.
Almost exactly the same time as he scampered over the air fence, Pedrosa set the fastest lap of the session, coming round in 1m56.858s.
Lorenzo eventually returned on his second bike but was unable to improve his time, finishing just five hundredths of a second down on Pedrosa.
As was the case in first practice, Tech 3's Andrea Dovizioso and Cal Crutchlow claimed third and fourth in a session punctuated by several falls.
Gresini's Alvaro Bautista, Aspar's Aleix Espargaro and Avintia's Yonny Hernandez were all casualties, with the latter causing a red flag when he punctured an air fence at Turn 5.
Despite his fall Bautista was still able to claim seventh, narrowly behind LCR Honda's Stefan Bradl and Ducati's Valentino Rossi, both of whom lapped within half a second of the ultimate benchmark.
Ben Spies was another early faller, although he was unharmed and returned to finish eighth fastest ahead of Espargaro and Toni Elias on the satellite Pramac Ducati.
Interwetten-Paddock’s Tom Luthi led the second Moto2 session from Alex de Angelis and Briton Scott Redding.
Blusens Avintia’s Maverick Vinales went quickest from Jakub Kornfeil and Briton Danny Kent in the afternoon Moto3 run-out.