The Italian, who lost both legs in a horrifying CART series crash in 2001, clocked a time of 12 minutes 11.13 seconds on the 16km course at the Kent circuit, beating nearest challenger Norbert Mosandl by over 13 seconds.
"This is a great accomplishment, one of the greatest of my life," Zanardi said. "I worked very hard to get here. It was great to live such an experience at 45."
Zanardi, who drove for Formula One teams including Jordan and Lotus in the early and mid-1990s, won two championship titles in the American CART series - formerly known as Indycar - in 1997 and 1998.
Williams then came calling to bring him back to Formula One, but once again he failed to perform as successfully in the worldwide series and returned to CART racing - only for tragedy to strike two seasons later.
After a poor start in a race at the EuroSpeedway Lausitz in Brandenburg, Zanardi was soon scything his way through the field when he tangled with another driver. The resulting spin put him straight in the path of Alex Tagliani, whose car took the front end of Zanard's car clean off - and with it both of Zanardi's legs.
Zanardi very nearly died. He lost three-quarters of his blood volume, but the efforts of doctors somehow saw him pull through - and even the loss of his legs did not slow him down. Though he would no longer race in 'open wheel' (F1-style) cars, he moved into touring cars where he was able to drive using prosthetic legs.
His first race came at Monza, in his native Italy, just two years after his crash, and he began driving full-time in first the European and then the World Touring Car Championship the year after, where he enjoyed a successful career that included several victories.
But the most extraordinary twist was yet to come: he had started handcycling as early as 2007, where he came fourth in the New York Marathon after just four weeks of training.
The idea of making it to the London 2012 Paralympics was then implanted in his head, and wins at marathons in Venice, Rome and New York in subsequent years earned him a spot on the team.
"Three years ago I stopped motor racing, at age 42," he said.
"It seemed a stupid thing to do to drop everything. It was against all odds. But it's not the first crazy thing I did in life. In the end I was right.
"You should not chase pipe dreams, but if you have a horizon to look into, happiness is just around the corner."
Zanardi was a former track record holder at Brands Hatch in the Formula 3000 category but admitted the circuit was hillier than he remembered.
"With an engine pushing me, I didn't realise it was so hilly. It was very hard, but if I had to design a course, this is what I would have done. It is beautiful, hard ... it suits my charcteristics of an old man," he said.
"When you are 40, you appreciate what you do every day. I enjoyed every day of training. I've had a magical adventure and this is a fantastic conclusion."
Almost 11 years to the day after his crash, Zanardi has become a Paralympic champion. In doing so, he has completed one of the most memorable recoveries ever seen in sport and become an inspiration to millions of people around the world.