Honda's Dani Pedrosa established himself at the top of the leaderboard with an early banker, before the Yamaha riders switched to the softer option tyres in the closing stages.
Points leader Valentino Rossi posted a 1m48.200s to briefly go fastest, only for Lorenzo to smash his best time, lapping the Spanish circuit in 1m47.517s, seven tenths clear of his team-mate and title rival.
Bradley Smith made it a 1-2-3 for Yamaha on the satellite Tech 3 bike, ahead of the factory Hondas of Pedrosa and Marquez in fourth and fifth, the pair having opted not to run the softer tyre.
Pol Espargaro was sixth on the second Tech 3 Yamaha, a tenth clear of his brother Aleix on the lead Suzuki and Andrea Dovizioso and Andrea Iannone on the factory Ducatis.
Scott Redding, fifth in the morning session, slipped to 12th on the timesheets, one spot ahead of LCR Honda's Cal Crutchlow.
FP1 AND FP2 TIMES