The Spaniard's 1m44.969s, set as the chequered flag fell, was comfortably faster than the rest of the field, led by his main title rival Dani Pedrosa.
The Honda rider had staged his own late rally, flying to the top of the timesheets with four minutes remaining. His best, a 1m45.215s, was itself a new record before Lorenzo blazed clear.
While pole position therefore boiled down to the typical protagonists, that scenario had looked unlikely earlier on as the session came alive with 20 minutes to run.
Ben Spies was the catalyst, jumping half a second clear with a 1m45.506s, at the time comfortably the fastest lap of the weekend.
Within moments Gresini's Alvaro Bautista, Tech 3 Yamaha's Andrea Dovizioso and Honda's Casey Stoner - riding through the pain of his Indianapolis injuries - had all responded and moved into the top four.
Cal Crutchlow then made his move, posting a new best - a 1m45.275s - to take provisional pole. At that moment, Lorenzo and Pedrosa were on the fringes of the second row and doing little to threaten.
New rubber provided the boost both needed however, culminating in a thrilling climax to an unpredictable session.
There was nearly further drama when Spies, running fourth, crashed at Turn 10 just as Lorenzo began his quick lap. The marshals managed to clear his bike however and Lorenzo was unobstructed en route to his pole time.
Spies was able to hang on to fourth, just fractions behind Crutchlow.
Bautista likewise kept fifth from Dovizioso, while Stoner – who had run as high as second – was relegated to seventh late on.
That was still enough to beat LCR's Stefan Bradl, who ran through the gravel early on, and works Ducati pair Valentino Rossi and Nicky Hayden, ninth and 10th respectively.