The Spaniard steered his Ferrari through puddles in poor visibility as drivers were spinning out of control during the qualifying session that was halted for 90 minutes by a torrential downpour.
Alonso — or any other Ferrari driver — has not topped Formula One's qualifying timesheets since the Singapore race in September 2010.
While it was difficult to complete each lap on Saturday, Alonso said, "I'm happy with pole position after nearly two years — for Ferrari it is a long time.
"With these weather conditions I think qualifying was probably one of the least important qualifying (sessions) of the whole year because things will likely get mixed up in the race," he added.
Alonso was just 0.047 seconds faster than Red Bull driver Mark Webber, who will start Sunday's race in the front row, alongside his main rival for the championship. Alonso has a 20-point lead over Webber.
It took an army of road sweepers to clear the racing track of pools of water, and drivers and team officials tried their best to entertain the rain-soaked fans.
Just before qualifying was halted during the second knockout section, Alonso span onto the rain-soaked grass. He was floating for split second, but managed to steer his car away from the wall and returned to the track.
"You are not in control of the car. You need a bit of luck and we were lucky today," the Spaniard said. "With that moment, with all the decisions that we make for the tires that it was the right one, and lucky also that we put the lap together, and lucky as well in the distance with Mark because there were some milliseconds."
Alonso's team is hoping the central England circuit will be spared a third day of rain storms for Sunday's race as he chases his third victory this season. At the European Grand Prix two weeks ago, the two-time world champion became the first driver to take the checkered flag for a second time in this unpredictable season.
"The weather forecast is rather uncertain, so we will have to be on high alert, ready to react to the slightest change," said Ferrari team principal Stefano Domenicali.
Michael Schumacher and Sebastian Vettel will both start from the second row on Sunday. And Schumacher was confident it could serve both Germans well, especially if it rains.
"Maybe I'm on the lucky side because it might be the slightly drier line compared to the inner side that's a little bit wet," Schumacher said.
The three-time British GP winner secured the third fastest time in his Mercedes, 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 either on intermediate or heavy wet (tires) so therefore rain is welcome tomorrow, " Schumacher said.
It was a miserable day for British drivers in front of a home crowd of about 60,000 fans.
Lewis Hamilton, who is third in the drivers' standings, qualified in eighth. His McLaren teammate, Jenson Button, was eliminated in the first qualifying section, finishing in 18th — his lowest grid position in 44 races.
But Button, who is eighth in the standings and has never won his home GP, 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," Button said.
Rob Harris can be reached at www.twitter.com/RobHarris