The win, gifted to him by Red Bull after world champion Sebastian Vettel was slowed by a wheelnut problem at his second pitstop, was the 27th of Alonso's career and lifted him level with the great Jackie Stewart in fifth position in the all-time lists.
Australian Mark Webber, who had started on pole position, finished third for Red Bull after trying to pass his teammate on the penultimate lap and then being told to maintain his position.
"I had two laps today with that (1951) car before the parade," said Alonso of Argentine Jose Froilan Gonzalez's historic Ferrari.
"Now 60 years later in the same circuit, with the same atmosphere and the same passion, winning again. I'm very proud...it made a special day." Vettel had hoped to chalk up a seventh win in nine races but still extended his overall lead over Webber, last year's winner at Silverstone who has yet to lead a lap this season, to 80 points from a previous 77.
McLaren's Lewis Hamilton entertained the fans by roaring from 10th on the grid to fourth, banging bodywork in a furious battle with Ferrari's Felipe Massa — who was forced wide — at the final corner.
Alonso took the lead on the 28th of the 52 laps when he pitted right behind Vettel, who had grabbed the lead off the grid. As the German's crew battled with the wheelgun, the Spaniard slipped past and was gone.
"It's hard to say how much we lost but surely we lost the lead. I think we had quite a cushion at that stage," said Vettel, who has still dropped only 21 points out of a possible 225, of the pit-stop drama.
"I think you have to accept fair and square that Ferrari beat us today...I think it shows us that we have to keep working and pushing very hard." Red Bull team boss Christian Horner recognized afterwards that "obviously Mark disagreed" with the order not to pass Vettel.
McLaren's Jenson Button's home-race jinx continued with the 31-year-old's hopes also wrecked by a wheelgun when he was waved away before the right front nut had been secured 12 laps from the end.
With the wheel wobbling wildly, he parked up at the pit lane exit and walked back to the garages without speaking to reporters.
The Briton has never yet stood on the F1 podium at Silverstone in 12 attempts.
