The Australian Red Bull driver is joined on the front row by McLaren’s Lewis Hamilton.
Webber’s Red Bull teammate and defending champion Sebastian Vettel is on the second row after posting the third quickest time, the German joined by the Ferrari of Fernando Alonso.
Red Bull were on target to fill the front row as they had done a fortnight ago in the British Grand Prix at Silverstone until Hamilton muscled in with a flying last lap at the Nurburgring circuit.
This is the third time this season that Webber has out-qualified Vettel, the runaway leader of this year’s championship.
Alonso’s Ferrari teammate Felipe Massa is on the third row alongside Mercedes’ driver Nico Rosberg with the second McLaren of Jenson Button and Force India’s Adrian Sutil on the fourth row.
Defending world champion Vettel topped the times in Saturday morning’s final free practice.
The Red Bull driver, who is also the runaway leader in this year’s title race, clocked a best time of one minute and 30.916 seconds in the final seconds of a closely-contested session run in cold conditions.
The 24-year-old champion’s best lap lifted him just clear of his team-mate Australian Mark Webber, by one-tenth of a second – but the Australian’s best lap was marred when he had to slow, ironically, because of Vettel.
Two-times champion Spaniard Fernando Alonso of Ferrari was third just two-tenths off the pace, having demonstrated he remains a major contender after winning the British Grand Prix two weeks ago.
Briton Lewis Hamilton was fourth for McLaren ahead of his team-mate and compatriot Jenson Button with German Nico Rosberg sixth in the leading Mercedes.
Brazilian Felipe Massa was seventh in the second Ferrari ahead of two more Germans, Adrian Sutil of Force India and seven-times champion Michael Schumacher, in the second Mercedes. Venezuelan Pastor Maldonado was 10th for Williams.
On a cool, overcast morning in the Eifel mountains, the air temperature was only 12 degrees Celsius and the track temperature just 22 degrees – making it the coldest circuit of the season to date, a major factor in the performance of the tyres.
Rosberg and his Mercedes team-mate Schumacher were the early pace-setters followed by Mexican Sergio Perez for Sauber and then Alonso. Rosberg responded, but then Alonso switched to the softer tyres to take over at the top again ahead of Webber and Hamilton.
But in the final minutes, Red Bull sent their men out on soft tyres and managed to take control of the top two positions.