The 34-year-old finished a shot clear of Tommy Fleetwood at the event in Scotland, played over three courses, capping a remarkable turnaround for a player who formerly occupied a spot in the top 50.
Wilson featured at the Ryder Cup in 2008 and had nine runner-up finishes to his name between 2006 and 2009.
However, a dip in form then saw him lose his European Tour card in 2012 and he began the Alfred Dunhill Links Championship ranked 792nd in the world.
Wilson is now back up to 156, having held off competition from the likes of Fleetwood, world number one Rory McIlroy and Richie Ramsay to claim his first title.
"Shooting eight under [at Carnoustie in the opening round] gave me some confidence and my confidence grew each day," Wilson explained.
"I've got good memories round here [St Andrews] - I finished second a few years ago alongside Rory when Simon Dyson won - so I knew what I had to do and I stood up and hit some really good shots.
"So my confidence from where it's been the last few of years is in a very different place right now."
Fleetwood moves up 10 places to 63rd courtesy of his second-place finish.
Paul McGinley, meanwhile, has been named the Race to Dubai European Tour Golfer of the Month for September, after captaining Europe to Ryder Cup glory at Gleneagles.
"I feel like there are 12 winners of the Golfer of the Month Award rather than me, but I'm delighted to accept this award on behalf of those 12 players who represented Europe so magnificently in The Ryder Cup at Gleneagles," he said.
"I'm very honoured and humbled to have been their Ryder Cup captain."