The reigning Silverstone champion was just 0.047 seconds faster than Red Bull driver Mark Webber, who will start Sunday's race alongside him on the front row and is his closest competitor in the championship.
"To complete a lap in these conditions was difficult, but I'm happy with pole position after nearly two years — for Ferrari it is a long time," said Alonso, who has a 20-point lead over Webber. "With these weather conditions I think qualifying was probably one of the least important qualifying of the whole year because things will likely get mixed up in the race."
Qualifying was halted during the second qualifying section and it took brooms and road sweepers to clear the track of standing water.
Even when qualifying resumed after more than 90 minutes, visibility was restricted on the central England circuit.
Despite the conditions, Michael Schumacher of Mercedes was able to secure the third fastest time, two weeks after coming third at the European GP for his first podium finish since coming out of retirement two years ago.
"We looked reasonably competitive in wet conditions," the German said.
Schumacher will start alongside world champion Sebastian Vettel, who qualified fourth in his Red Bull.
It was miserable afternoon, though, for the leading British drivers.
Lewis Hamilton, who is third in the drivers' standings, qualified in eighth, while McLaren teammate Jenson Button was eliminated in the first qualifying section, and will start 18th, his lowest grid position in 44 races.
But Button, who is eighth in the standings, was able to save his wet and intermediate tires which could bode well for Sunday's race.
"We don't get many tires so (failing to reach final qualifying) probably is not a bad thing," he said. "If the weather is wet tomorrow, as we think it is going to be, we haven't done so much mileage on the tires whereas now they are going to be running round for two more sessions."
