The Spaniard carried on his morning momentum to put Yamaha top early on, but just three minutes in he was flicked off his bike at Turn 10 and landed on the left collarbone he broke at Assen.
He spent the remainder of the session in the medical centre undergoing checks. No information about his condition has yet been released.
Cal Crutchlow also crashed heavily, losing the front of his Tech 3 Yamaha on a bump just before the apex of the downhill Turn 11.
He was sent flying through the gravel and, after his won trip to the medical centre, did not head back out.
In the pair's absence, the pace was set by home favourite Stefan Bradl on the satellite LCR Honda.
Works rider Dani Pedrosa snatched second from stable-mate Marc Marquez as the chequered flag fell.
Lorenzo meanwhile was fourth fastest, just one thousandth of a second slower than Marquez and within 0.25s of Bradl.
His Yamaha team-mate Valentino Rossi, who triumphed last time out in the Dutch TT, was fifth ahead of Nicky Hayden, Aleix Espargaro and Andrea Dovizioso.
Hayden, who saved a massive tank-slapper in FP1, made another remarkable recovery to prevent crashing early on at Turn 9.
His clean run came to an end late on however when he lost his Ducati at Turn 3, mirroring Bryan Staring's earlier off at the same corner.
- Sports & Recreation
- Stefan Bradl