Like many of the other frontrunners, the American had elected to sit out the first session when the track was neither fully wet nor fully dry.
He was first out at the start of the second however, when all uncertainty about conditions had been removed by a brief but heavy shower.
Times fell consistently as the session developed, and in the final minutes top spot almost exclusively belonged to Yamaha's two works riders.
Lorenzo looked to have sealed it with the session's first sub 2m01s lap, but moments later Spies shaved a further five tenths of the Spaniard's benchmark to go top.
There was still time for Honda's Dani Pedrosa to sneak into second, just six hundredths of a second shy of Spies.
Lorenzo stayed third ahead of Ducati's Nicky Hayden, the last rider to get within one second of the ultimate pace.
Tech 3 Yamaha's Andrea Dovizioso were fifth and seventh, sandwiching the LCR Honda of Stefan Bradl.
Valentino Rossi on the second Ducati locked out ninth, ahead of satellite riders Karel Abraham (Cardion Ducati), Alvaro Bautista (Gresini Honda) and the second works Honda of Jonathan Rea.