The Spaniard led for the majority of the session but saw his new lap record surpassed by defending champion Stoner with less than a minute remaining.
Not to be outdone, the Yamaha driver dialled in a scintillating 1:20.554 to claim the 21st pole of his career and the first for his team since Jerez in April.
Stoner, who still harbours hopes of winning back-to-back titles, was left furious at the end and blamed back markers, notably CRT rider Danilo Petrucci, for ruining his pole chances.
“I never got one clean lap," he said. "Everyone was just sitting in the middle of the road and just not looking over their shoulders. I’m sick of it. I’m over it. With such a short, dusty track it’s just too dangerous.”
Repsol Honda’s Dani Pedrosa, who set the pace after Friday afternoon’s session using a new frame and engine, was third quickest from home favourite Ben Spies but suffered a big off at turn 3 with 10 minutes remaining although he walked gingerly away from his bike.
Britain’s Cal Crutchlow starts from fifth ahead of Andrea Dovizioso, Alvaro Bautista and two-time Laguna Seca winner Nicky Hayden with Valentino Rossi 10th.
1. Jorge Lorenzo (Spain) Yamaha 1:20.554
2. Casey Stoner (Australia) Honda 1:20.628
3. Dani Pedrosa (Spain) Honda 1:20.906
4. Ben Spies (U.S.) Yamaha 1:21.094
5. Cal Crutchlow (Britain) Yamaha 1:21.268
6. Andrea Dovizioso (Italy) Yamaha 1:21.539
7. Alvaro Bautista (Spain) Honda 1:21.732
8. Nicky Hayden (U.S.) Ducati 1:21.734
9. Stefan Bradl (Germany) Honda 1:21.753
10. Valentino Rossi (Italy) Ducati 1:22.544