Damp and very cold conditions dissuaded most of the prototype field from coming out, meaning the timesheets were dominated by CRT riders.
Petrucci's late 1m43.178s on the Suter-BMW that Ioda has switched to this weekend put him 0.2 seconds ahead of Michele Pirro's Gresini FTR-Honda.
James Ellison completed the top three on Paul Bird's Aprilia.
Fourth went to newcomer David Salom, replacing Ivan Silva in the Avintia line-up.
Only two prototype riders set times: Yamaha's Ben Spies in fifth and Ducati's Nicky Hayden in seventh.
Title rivals Jorge Lorenzo and Dani Pedrosa, and Casey Stoner's stand-in Jonathan Rea, were among the large number of riders who preferred to wait for better conditions later on.