The world championship leader set a 1m48.076s early on, and that proved unbeatable. He lost some track time after running straight on at the first corner, San Donato, and eventually having to let his Yamaha tip over, but was soon back on the circuit doing consistent 1m48s lap.
Casey Stoner was only sixth on the other works Honda, although his final run was a troubled one - with traffic on one flying lap and a minor error on the next.
Hector Barbera impressed on the Pramac Ducati with fourth position, achieved solo rather than in a group of riders. The Spaniard was riding his spare bike by that time following an accident at the Casanova/Savelli esses that ended with his Ducati landing on the circuit after tumbling down the edge of the track.
A five-minute stoppage was required to clear up debris. Barbera was quickly thrown clear and was unhurt.
Other incidents included Alvaro Bautista crashing his Gresini Honda at San Donato, where Randy de Puniet (Aspar Aprilia) also had a trip off the road, and Avintia rider Ivan Silva having a fall.
Between Barbera and Stoner, Andrea Dovizioso was top Tech 3 Yamaha rider in fifth.
Valentino Rossi was the slowest of the three Ducati riders in ninth.
1. Jorge Lorenzo Yamaha 1m48.076s
2. Dani Pedrosa Honda 1m48.107s + 0.031
3. Nicky Hayden Ducati 1m48.157s + 0.081
4. Hector Barbera Ducati 1m48.254s + 0.178
5. Andrea Dovizioso Yamaha 1m48.308s + 0.232
6. Casey Stoner Honda 1m48.527s + 0.451
7. Ben Spies Yamaha 1m48.540s + 0.464
8. Cal Crutchlow Yamaha 1m48.650s + 0.574
9. Valentino Rossi Ducati 1m49.017s + 0.941
10. Stefan Bradl Honda 1m49.022s + 0.946
11. Alvaro Bautista Honda 1m49.208s + 1.132
12. Aleix Espargaro Art 1m50.015s + 1.939
13. Randy De Puniet Art 1m50.269s + 2.193
14. Michele Pirro Ftr 1m51.130s + 3.054
15. Yonny Hernandez Bqr 1m51.322s + 3.246
16. Mattia Pasini Art 1m51.384s + 3.308
17. Colin Edwards Suter 1m51.857s + 3.781
18. James Ellison Art 1m51.966s + 3.890
19. Danilo Petrucci Ioda 1m52.109s + 4.033
20. Ivan Silva Bqr 1m52.558s + 4.482