A delighted Webber said: "This is a very special day for me. I've been close to getting pole a few times in the past, and now we're here.
"The team has done a very good job; I've been quick all weekend, but we got really tested today.
"All the teams and drivers did in that session - it was very chaotic. But I'm now in a fantastic position to get my first win. Obviously the Brawns have had a strong season and will push us.
"But we're up for the fight - I certainly am - and I'm up for trying to win my first race."
Rain blighted the middle 15-minute session at the Nurburgring, but it stayed dry for the vital top-10 shootout, and it was the Australian due to make his 130th start who heads the field.
Red Bull Racing's Webber then had to anxiously wait in the dying moments as the Brawns of Rubens Barrichello and championship leader Button made it a double act on the grid with second and third.
Button said: "We're struggling with the tyres any way, but when you chuck water in there as well it's quite difficult.
"But it's great to see us, Rubens and myself, in the top three - and Mark's got his first pole, so congratulations to him.
"Tomorrow is going to be an interesting one. The weather is going to be similar to today - wet and dry - so with a little bit of luck, we'll make the best of the situation."
But Webber's Red Bull team-mate Sebastian Vettel, who won the British GP at Silverstone, is also up there in fouth.
Lewis Hamilton proved his practice performances of yesterday and this morning were no flukes, the world champion starting fifth in his much-improved McLaren.
Grid positions after qualifying: 1 Mark Webber (Aus) Red Bull 1min 32.230secs, 2 Rubens Barrichello (Bra) Brawn GP 1:32.357, 3 Jenson Button (Gbr) Brawn GP 1:32.473, 4 Sebastian Vettel (Ger) Red Bull 1:32.480, 5 Lewis Hamilton (Gbr) McLaren 1:32.616, 6 Heikki Kovalainen (Fin) McLaren 1:33.859, 7 Adrian Sutil (Ger) Force India 1:34.316, 8 Felipe Massa (Bra) Ferrari 1:34.574, 9 Kimi Raikkonen (Fin) Ferrari 1:34.710, 10 Nelson Piquet Jr. (Bra) Renault 1:34.803, 11 Nick Heidfeld (Ger) BMW Sauber 1:42.310, 12 Fernando Alonso (Spa) Renault 1:42.318, 13 Kazuki Nakajima (Jpn) Williams 1:42.500, 14 Jarno Trulli (Ita) Toyota 1:42.771, 15 Nico Rosberg (Ger) Williams 1:42.859, 16 Robert Kubica (Pol) BMW Sauber 1:32.190, 17 Sebastien Buemi (Swi) Scuderia Toro Rosso 1:32.251, 18 Giancarlo Fisichella (Ita) Force India 1:32.402, 19 Timo Glock (Ger) Toyota 1:32.423, 20 Sebastien Bourdais (Fra) Scuderia Toro Rosso 1:33.559
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