Only 13 riders ended up setting times, among them the four Ducati prototypes and the two satellite Hondas.
The rest of the frontrunners, including the fastest six riders from the morning session, all put in sighting laps and then sat out the session, with conditions too wet for slicks and too dry for wets.
For much of the session times therefore did not change, leaving Gresini's Alvaro Bautista at the top, fractions ahead of Valentino Rossi.
Six minutes from the flag however slicks suddenly yielded massive gains, allowing those with the inclination the chance to go out and cut swathes from the previous bests.
While the shift in conditions still came too late for the prototype riders, there were plenty of CRT riders ready to head out, with Silva leading the way.
Aspar's Randy de Puniet and Speed Master's Roberto Rolfo followed suit and helped lower the benchmark, before Silva settled matters with a 2m10.602s.
That was more than a second clear of Gresini's Michele Pirro, de Puniet and Rolfo, and over five seconds faster than Karel Abraham on the leading prototype machine.
Bautista and Rossi, neither of whom ventured out on slicks, finished sixth and seventh, ahead of Aleix Espargaro, Nicky Hayden, James Ellison and Stefan Bradl.
- Alvaro Bautista