World champion Casey Stoner overcame handling problems, a heavy practice fall and qualifying showers to take a surprise pole position for the Dutch MotoGP at Assen.

The Australian shot from ninth to third with just minutes remaining, then blasted to the top by half-a-second from Repsol Honda team-mate Dani Pedrosa on his penultimate lap.

Title leader Jorge Lorenzo briefly knocked Pedrosa from second, but the #26 retaliated to seal an RCV one-two by closing to within 0.115s of Stoner.

Honda LCR rookie Stefan Bradl provided a final surprise by jumping into fourth place, aided by a last-lap tow from Valentino Rossi.

Stoner had struggled to tenth place with chatter problems on Thursday afternoon, before suffering a punishing highside - "one of the biggest in my career and certainly one of the most painful" - due to a rain shower in Friday morning's final practice session.

Rain was again a threat from the start of qualifying, prompting flat out action from the off.

MotoGP title leader Lorenzo got off to a flying start by setting his best lap of the event in the opening five minutes, then posting further successive improvements.

But practice pace setter Pedrosa was also on a charge, matching Lorenzo's improvements before finally leap-frogging his fellow Spaniard to take provisional pole after twelve minutes of the hour.

And then the rain spots arrived, initially sending all 21 riders back to the pits. The moisture continued off and on for most of the session, containing lap times until a window of opportunity opened in the closing minutes.

Stoner explained that his dramatic end-of-session improvement had also been down to switching from the harder rear tyre, which he has struggled to make work, to the softer rear tyre.

"It was certainly a lap that surprised us. The pace is there we just need to make sure we can last the race," he said.

Bradl, who got within 0.034s of Lorenzo, will be joined on row two by Yamaha Tech 3 rider Cal Crutchlow and defending Assen winner Ben Spies (Factory Yamaha).

Crutchlow's team-mate Andrea Dovizioso was the final rider to lap within one-second of pole, with a late fall for Silverstone pole sitter Alvaro Bautista leaving the Honda Gresini rider just behind the Italian in eighth.

Factory Ducati riders Nicky Hayden and Valentino Rossi qualified ninth and tenth, with the satellite GP12 of Hector Barbra in eleventh.

0.541s separated Barbera from the top CRT of Randy de Puniet, who got the better of Aspar Aprilia team-mate Aleix Espargaro by 0.177s.

The Assen circuit is the only survivor from the inaugural 1949 World Championship calendar. The Dutch TT is traditionally held on the last Saturday in June, Sunday racing having originally been frowned upon for religious reasons.

Lorenzo starts Saturday's race with a 25-point advantage over Stoner. Lorenzo (4) and Stoner (2) are the only riders to win races so far this year.

Qualifying:

1. Casey Stoner
2. Dani Pedrosa
3. Jorge Lorenzo
4. Stefan Bradl
5. Cal Crutchlow
6. Ben Spies
7. Andrea Dovizioso
8. Alvaro Bautista
9. Nicky Hayden
10. Valentino Rossi
11. Hector Barbera
12. Randy De Puniet
13. Aleix Espargaro
14. Michele Pirro
15. Mattia Pasini
16. Danilo Petrucci
17. Karel Abraham
18. Yonny Hernandez
19. James Ellison
20. Ivan Silva
21. Colin Edwards