The Spaniard, who was defeated by Lorenzo in Sunday's grand prix, bounced back from a late crash at Turn 12 to hit the front in the final moments of the day.
A 1m33.264s put him just over two tenths clear of Lorenzo, who was a similar gap ahead of team-mate Valentino Rossi.
The Yamaha pair both ran a YZR-M1 in 2014 configuration, although it was not a full prototype machine.
Honda meanwhile brought an evolved version of the 2014 bike Marc Marquez and Dani Pedrosa tested at Aragon in June.
While Marquez went fastest, Pedrosa could only manage sixth overall, some six tenths off the pace.
Tech 3's Cal Crutchlow - who focused on brake improvements - and Gresini's Alvaro Bautista were both faster than the works Honda rider.
Suzuki was also present with Randy de Puniet, and used the test to trial a different specification engine and to define its development paths.
The Frenchman ended the day 13th fastest, just less than two seconds down on Marquez.
Andrea Dovizioso finished eighth fastest on the revised Ducati GP13, which features a new chassis.
Ducati were unable to provide Nicky Hayden with the same equipment, although the American was just 0.1s off his team-mate's best.
Andrea Iannone ended the day 10th for the satellite Pramac team, while team newcomer Yonny Hernandez - set to stand in for the injured Ben Spies in forthcoming races - was 16th.