After taking top spot on the grid a fortnight ago in the rain at Silverstone, Alonso has now put his Ferrari on pole in back-to-back races, and for the 22nd time in his Formula One career.
The Spaniard was comfortably quicker by half a second than local hero Sebastian Vettel, born just 28 miles away in Heppenheim.
Reigning world champ Vettel was forced to settle for second, with Red Bull teammate Mark Webber third, although the Australian has to serve a five-place grid penalty for a gearbox change.
Webber’s penalty means Michael Schumacher jumps up to third in his Mercedes and is joined on the second row by another German in Force India’s Nico Hulkenberg.
Williams’ Pastor Maldonado will start fifth, and then come McLaren duo Jenson Button and Lewis Hamilton, the former out-qualifying the latter for the first time this season.
However, the duo both proved their tyres struggle in the wet as they found themselves three and a half seconds off the pace of Alonso on the full-wet Pirelli tyres.
Sahara Force India’s Nico Hulkenberg produced his season’s best qualifying performance by setting the fifth fastest time at the Formula One German Grand Prix here on Saturday while his teammate Paul di Resta was ninth fastest amid wet conditions at the Hockenheimring
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