Andrea Iannone secured a maiden MotoGP pole position on home soil at Mugello, while Marc Marquez will start from 13th after getting knocked out of the first part of qualifying.
Marquez left himself with work to do after setting only the 11th quickest practice time in FP3, ensuring he would have to battle his way into Q2, and further demonstrated his factory Honda's demons with a lowside crash at the first corner in FP4 immediately before qualfying.
The reigning champion waited until the middle of the 15-minute Q1 session to hit the track, immediately going second to Suzuki's Aleix Espargaro, 0.018s slower, and then failing to improve on his following lap.
That left Marquez vulnerable as the rest of the field hit the track in the closing minutes, and it fell to Pramac Ducati's Yonny Hernandez to seal the Spaniard's fate.
Helped by a tow from Loris Baz, Hernandez set the fastest time of all, beating Espargaro by a tenth, to secure his Q2 spot at the expense of Marquez, who will have to battle his way up the order from 13th in Sunday's race.
Lorenzo misses out
Lorenzo was quickest initially in Q2, setting a benchmark of 1m46.808s before lowering it to a 1m46.648s in the closing minutes - but he was immediately beaten by Iannone's Ducati, benefitting from the softer rear tyre and the Yamaha rider's tow.
The Italian's 1m46.489s proved enough for pole, with Lorenzo missing out by 0.095s in his final attempt. Andrea Dovizioso, also on the soft rear, secured the final front row spot in third, 0.121s back from teammate Iannone.
Cal Crutchlow, who held the spot early on, was demoted to fourth, with Espargaro and Ducati wild-card Michele Pirro, who enjoyed Dovizioso's tow on his best lap, making up the rest of the second row.
Repsol Honda's Dani Pedrosa took seventh, ahead of a slightly subdued Valentino Rossi aboard the second factory Yamaha and Suzuki's Maverick Vinales, who equalled his best ever MotoGP grid position with ninth.
Tech 3 Yamaha men Pol Espargaro and Bradley Smith and Hernandez complete the top dozen ahead of Marquez.
|16||Stefan Bradl||Yamaha Forward||1.558|
|18||Loris Baz||Yamaha Forward||1.644|
|22||Mike Di Meglio||Ducati||2.014|
|25||Alex de Angelis||ART||2.709|