The Italian, a seven-time world champion in the top class, has not won a race since the 2010 Malaysian Grand Prix, and just two weeks ago suffered the indignity of tumbling out of his home race on the opening lap.
But the 34-year-old showed some of the old magic remains as his late fast lap of one minute 42.297 seconds jumped him from the middle of the pack to the top of the standings.
Lorenzo, looking to close his 12-point deficit to championship leader Dani Pedrosa, had topped the times for much of the session and had led the way in the morning running, but eventually missed out to his team-mate by just under five hundredths of a second.
Pedrosa was next up on the first of the Repsol Hondas, with Britain’s Cal Crutchlow fourth overall aboard his Tech 3 Yamaha. Alvaro Bautista took a superb fifth on the satellite Gresini Honda machine with Marc Marquez sixth and Nicky Hayden and Andrea Dovizioso seventh and eighth.
Crutchlow’s team-mate Bradley Smith, nursing the hand and wrist injuries he suffered two weeks ago, was 14th after another crash which he limped away from.