After a dry Q1, qualifying was shaken up by rainfall just before the second session started.
Alonso had indicated to his team that he thought the top 10 shoot-out should be delayed, just as qualifying had been at Silverstone last time around in the rain, but it began as scheduled and the championship leader proved himself the quickest man on track regardless.
The Spaniard's lap of 1:40.621 was four-tenths of a second clear of his nearest challenger, Red Bull's Sebastian Vettel. Mark Webber, the closest to Alonso in the championship race, was third, but will lose five places for a gearbox change.
That paves the way for an all-German second row at the home Grand Prix, with veteran Michael Schumacher ahead of youngster Nico Hulkenberg.
Pastor Maldonado managed to get his Williams into fifth, a place ahead of Jenson Button, who out-qualified Lewis Hamilton for the first time this season.
Paul di Resta and Kimi Raikkonen rounded out the top 10.
The rain had threatened qualifying from the very beginning, with dark skies overhead forcing the drivers out immediately, but Q1 escaped the rain and the session was contested in the dry.
It was rookie Jean-Eric Vergne who missed out along with the familiar tail-enders from progressing to the second part of qualifying, but Schumacher was very fortunate to get across the line just six-hundredths of a second quicker than the Frenchman to take 17th place.
Intermediate tyres were the order of the day in Q2, and Schumacher's performance improved immeasurably, sitting comfortably near the top of the timesheets with the McLarens, Alonso and Vettel as his team-mate Nico Rosberg fell well short in 17th.
Romain Grosjean, who had laboured in the Lotus all day, also bowed out, along with Ferrari's Felipe Massa.
Rosberg put on a set of wet tyres in a vain attempt to compete, but the track was getting more slippery and there was no chance of improving on his times.
By Q3 wet tyres were essential, with standing water on the track, but the rain had ceased and the conditions improved as the time ticked away.
It was treacherous, with several laps started and aborted after running wide, but Alonso, the championship leader, was untouchable. He set the two fastest times of the session, and he will now fancy his chances of extending his advantage in the title race come Sunday's Grand Prix.