The Althea Ducati rider's best lap of one minute 54.144 seconds was set early in the Superpole session but was nevertheless sufficient to see off his rivals.
The Spaniard, who leads Max Biaggi by 62 points after his double win at Silverstone at the end of July, took his fifth pole of the season by four tenths of a second from Ireland's Eugene Laverty (Yamaha), who sits fourth in the riders' standings.
The Aprilia of reigning champion Biaggi will start from third on the grid despite the Italian riding with an injury to his left foot, while Marco Melandri (Yamaha World Superbike Team) completes the front row.
Melandri sits third in the championship race and is chasing his fourth win of 2011.
Noriyuki Haga (Pata Aprilia), a previous Nurburgring winner, will start from fifth place ahead of Tom Sykes (Kawasaki), while Leon Haslam (BMW Motorrad Motorsport) and Sylvain Guintoli (Effenbert Liberty Ducati) also start from row two.
Irishman Jonathan Rea was only ninth quickest but had something to celebrate after signing to stay with the Castrol Honda team for the 2012 season.
Rea said: "I'd like to thank Honda for the continued support and the team for everything they do for me. Together, we all have unfinished business in the World Superbike championship."