Stoner had looked to be on course for top spot in the timings but a phenomenal last lap of the session from Yamaha man Lorenzo put him 0.074s in front of the reigning World Champion on the starting grid for Round 10.
Lorenzo had already broken Stoner's outright lap record at the circuit – a time of 1'20.700 which had stood since 2008 – before the Repsol Honda rider responded by lowering the bar even further. Lorenzo then hit back at the very death with a superb 1'20.554 to snatch pole and set the scene for a fantastic race.
'We had the potential to be on pole, but we weren't able to show that because there was too much traffic' - Casey Stoner
After a final practice session in the morning which was largely lost to fog, Lorenzo was happy to have been able to ride for the full hour of QP in the afternoon and said: “It was great to take advantage of the entire qualifying because in the morning we couldn't. We tried both rear tyres [but] we're still unclear on which will be best for tomorrow's race.
“The race is going to be one of the hardest all season because 32 laps is a lot, we never stop, we're always taking corners. It's very demanding, so maybe the rider who's freshest at the start of the race will have a big advantage tomorrow.”
Stoner was frustrated by on-track traffic which upset his rhythm, although he is looking forward to the race – which he won last year.
“We definitely had the potential to be on pole today, but we weren't able to show that because there was too much traffic,” he said, before turning his attentions to the race.
“There's no breather here but I actually find it less physically demanding than other circuits. We don't have as much chatter on this circuit because we're going left, and that makes it a bit easier because we don't have to put the same amount of effort in.”
Stoner's Repsol Honda team-mate and fellow Red Bull-backed rider Dani Pedrosa completed the front row with the only other sub-1'21” lap of the session, as he sought to maximise the benefits of the fully revised RC213V machine he has been running this weekend.
“We had a lot of work this afternoon because we didn't go out this morning. We were busy for the whole session,” he explained, adding after that he was enjoying the new version of his machine.
“I have a good feeling with the engine and the chassis,” he said. “I still don't know [the bike] perfectly 100%, but it's a good feeling so I'm confident.”
It was an all-Yamaha second row with factory rider Ben Spies and satellite Tech 3 team pair Cal Crutchlow and Andrea Dovizioso all inside the top six. Spies had a heavy crash at Turn 3 towards the end of the session from which he stumbled away, and he turned up for the post-qualifying press conference on crutches.
An impressive display from Stefan Bradl in his first qualifying at Laguna Seca saw the German take ninth on the grid, behind Álvaro Bautista and Nicky Hayden but ahead of Valentino Rossi.
Straight after qualifying there was a fantastic show on the start/finish straight, in which a stunt rider was pulling no-handed wheelies as part of a daring set of tricks. Not for the feint-hearted!
Here's how they line up for Sunday....
1. Jorge Lorenzo (SPA), Yamaha, 1'20.554
2. Casey Stoner (AUS), Repsol Honda, 1'20.628
3. Dani Pedrosa (SPA), Repsol Honda, 1'20.906
4. Ben Spies (USA), Yamaha, 1'21.094
5. Cal Crutchlow (GBR), Tech 3 Yamaha, 1'21.268
6. Andrea Dovizioso (ITA), Tech 3 Yamaha, 1'21.539
7. Álvaro Bautista (SPA), Gresini Honda, 1'21.732
8. Nicky Hayden (USA), Ducati, 1'21.734
9. Stefan Bradl (GER), LCR Honda, 1'21.753
10. Valentino Rossi (ITA), Ducati, 1'22.544