While most riders left it until the final minutes to bolt on soft rubber, Stoner (Honda) made his move with eight minutes to go, dropping down to a 1m41.295s - at the time enough to go more than three tenths clear of the field.
There was still plenty of time for him to be deposed, but his benchmark ultimately proved too much, earning the reigning champion only his second MotoGP pole at Barcelona.
Yamaha's Lorenzo came closest to snatching top spot, moving into second in the final two minutes. The Spaniard had time for one more run but opted to sit up early on in the lap.
Few were left on circuit to challenge Stoner. Tech 3 Yamaha's Cal Crutchlow had already set his own best, enough to take second before Lorenzo's late charge.
The Briton still did enough to secure the final place on the front row, ahead of the second works Yamaha of Ben Spies, who equalled his best qualifying performance of the year in fourth.
Dani Pedrosa, one of the favourites for pole, spoiled his final run when he ran wide and through the gravel at Turn 10. The Honda rider was forced to settle for fifth, ahead of the second Tech 3 Yamaha of Andrea Dovizioso.
Nicky Hayden and Valentino Rossi's works Ducatis will start on the third row in seventh and ninth, separated in the final minute by LCR Honda's Stefan Bradl.
Gresini Honda's Alvaro Bautista took 10th ahead of the satellite Pramac and Cardion Ducatis of Hector Barbera and Karel Abraham.
Aspar's Randy de Puniet meanwhile finished as top CRT rider in 13th, ahead of the returning Colin Edwards (Forward), who missed the previous round at Le Mans due to injury.