Lorenzo had been quickest in all three practice sessions and for the majority of qualifying. Pedrosa edged 0.058 seconds ahead of him with a 1:47.365 in the closing minutes, but Lorenzo's Yamaha was on course to depose the Honda for the first three sectors of his final lap before abandoning it and angrily pulling into the pits, slamming his hand on the front of his bike in displeasure as he did so.
In a session full of surprises, Pramac Ducati Hector Barbera secured the first front row start of his MotoGP career in third place, beatings works Ducati rider Nicky Hayden.
Honda's Casey Stoner was only fifth, having been off the pace throughout the hour. The Australian never looked like a pole contender, having also been unhappy with his bike in Friday practice.
Cal Crutchlow recovered from a late crash at the Correntaio corner to beat Tech 3 Yamaha team-mate Andrea Dovizioso to sixth with his last lap.
Ben Spies had a similar accident to Crutchlow on the second works Yamaha, and could only qualify ninth, between Stefan Bradl (LCR Honda) and Valentino Rossi (Ducati).
Alvaro Bautista's miserable weekend continued as he took 11th on the Gresini Honda.
Aleix Espargaro beat Aspar Aprilia team-mate Randy de Puniet by just 0.063s in the battle for CRT honours.