Going out second last in blistering heat at his home track, Heidfeld clocked 1:30.081 to edge out McLaren's Kimi Raikkonen by 0.116 seconds.
It was the first pole position for BMW-powered Williams since Ralf Schumacher's at the Canadian Grand Prix last June.
"It's fantastic," said Heidfeld, who was second in Monaco last week. "The first time I've had pole position in Formula One and at my home race at the Nuerburgring, it couldn't be better."
"After Monaco, I thought it would be more difficult here. I thought we would probably be on the second row."
Finn Raikkonen, who had been on pole for the last three races and won two of them, will join the German on the front row for Sunday's race with Heidfeld's Australian team mate Mark Webber and Toyota's Jarno Trulli sharing the second row.
"Obviously we would have preferred to have been first but today we weren't able to do it today," said Raikkonen.
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Championship leader Fernando Alonso was sixth fastest for Renault and will be on row three with Colombian Juan Pablo Montoya, who was fifth for McLaren.
Ferarri's world champion Michael Schumacher, the winner from pole position here last year, had another disappointing day and will be on the fifth row of the grid in 10th place.
POOR DAY
BAR also had a poor day on their return to action after a two-race ban, hampered by being forced to go out first in the session because of their absence from the last race.
Briton Jenson Button, third here last year, qualified 13th while his Japanese team mate Takuma Sato, who started on the front row last year, was 16th fastest.
Qualifying for the seventh round of the 19-race championship was held over a single session because of widespread dissatisfaction with the format in the previous six rounds, when there was a second session on the morning of the race.
Raikkonen, who trails Spaniard Alonso by 22 points in the drivers' standings, said not having his rival in the front two rows was a boost but that the new qualifying system made the grid less of an indication of how the race might go.
"Before you all went on light fuel but now we don't know what strategy other teams are on," he said. "It's better to have a Williams up here rather than the Renault, but maybe they have more fuel."
Heidfeld was just delighted to start from the front of the grid for the first time after five years in Formula One.
"You can't wish for more than pole position, whatever strategy you are on, and so we are happy," he said.
Qualifying result:
1. Nick Heidfeld (Germany) Williams 1:30.081
2. Kimi Raikkonen (Finland) McLaren 1:30.197
3. Mark Webber (Australia) Williams 1:30.368
4. Jarno Trulli (Italy) Toyota 1:30.700
5. Juan Pablo Montoya (Colombia) McLaren 1:30.890
6. Fernando Alonso (Spain) Renault 1:31.056
7. Rubens Barrichello (Brazil) Ferrari 1:31.249
8. Ralf Schumacher (Germany) Toyota 1:31.392
9. Giancarlo Fisichella (Italy) Renault 1:31.566
10. Michael Schumacher (Germany) Ferrari 1:31.585
11. Felipe Massa (Brazil) Sauber 1:32.205
12. David Coulthard (Britain) Red Bull 1:32.553
13. Jenson Button (Britain) BAR 1:32.594
14. Vitantonio Liuzzi (Italy) Red Bull 1:32.642
15. Jacques Villeneuve (Canada) Sauber 1:32.891
16. Takuma Sato (Japan) BAR 1:32.926
17. Tiago Monteiro (Portugal) Jordan 1:35.047
18. Patrick Friesacher (Austria) Minardi 1:35.954
19. Narain Karthikeyan (India) Jordan 1:36.192
20. Christijan Albers (Netherlands) Minardi 1:36.239