Stoner claims Japanese pole
Qualifying proved to be an engrossing battle between Stoner, his Honda works team-mate Dani Pedrosa and Lorenzo, with the trio often separated by less than 0.1s.
Pedrosa was the first rider to dip below 1m46s, but as has so often been the case this season Stoner was able to respond, moving more than two tenths clear at the front.
With five minutes to go however his position suddenly came under serious threat, as Lorenzo produced a stunning lap on the Yamaha to take provisional pole, beating his own 2008 lap record in the process.
Once again it was up to Stoner to respond, and while his first lap fell short his second flyer was phenomenal, the Australian eventually posting a 1m45.267s to shatter the lap record and move more than a quarter of a second clear.
Lorenzo therefore had to settle for second, while Andrea Dovizioso - pole-sitter last year - demoted Pedrosa in the final minutes to capture the final spot on the front row.
Pedrosa will share the second row with Yamaha's Ben Spies and Gresini's Marco Simoncelli.
Spies, battling severe illness and sickness, improved throughout to seal fifth, while Simoncelli was able to seal sixth on his final lap, having lost his first bike when he dropped the front at Turn 5 in the first 25 minutes.
Simoncelli's gain was Valentino Rossi's loss, the Italian dropping to seventh having just set his own late flyer. Rossi was often troubling the top six however, hinting at real progress for Ducati.
There was a fall too for Tech 3's Colin Edwards, although like Simoncelli he was able to return and use a second bike, eventually finishing 14th fastest.