The 24-year-old amateur, who held a two shot lead on the 18th tee, delivered the grandstand finish with a perfect shot to within 30cm of the hole to card a four under par 68 and seal the win.
About an hour earlier on the 18th, World No.1 Lydia Ko underlined her class with a 5m birdie putt to break her course record at the West Auckland links by two shots with a seven under 65 and defend her title by an incredible 17 shots.
But it was the battle between good mates Wilkin and Fox that attracted the biggest gallery in the warm conditions at Muriwai.
Wilkin, who thought he only held a one shot lead, walked up the18th acknowledging the applause by waving his cap to the crowd on the banks to celebrate the biggest win of his amateur career.
"This is pretty exciting for me," said an emotional Wilkin after the round.
"Today was a bit of a blur. It hasn't really sunk in yet. It is a really good step forward for me and where I want to be if I want to turn professional at the end of the year to start playing for money to know that I am there or thereabouts is pretty pleasing."
Wilkin joins an elite club of amateurs to win on the Charles Tour that includes Josh Geary, Troy Ropiha, Ben Campbell and Josh Munn.
He made it tense by missing a 1.5m putt on the 17th to only lead by two shots with one hole to play. Wilkin was in two minds until he committed to being attacking.
"I couldn't decide whether I was going to hit two iron or driver. I knew Foxy was wide enough to have a good shot at the green. In situations like those you have to really trust yourself. I just teed up drive and let rip."
It paid off as he set up the opportunity to deliver the championship winning shot.
"To be honest I did pull it a little bit, it did spin right, but I was playing for that backboard and I pulled it off. I would have been happy to get it on the back tier and two putt, but to do it like that was great.
"It was awesome walking up the 18th especially with how close my shot was. I didn't have a nervy putt. After missing a five footer on 17 it was a great release I guess."
Fox, who finished runner-up in a Charles Tour event for the second time in succession in 2012, and third overall, was naturally disappointed but paid credit to Wilkin.
"Fraser's one of my best mates and as much as I like winning if anyone else was going to win, he was the guy I was pulling for. It was great to see him win and the way he did it was very impressive "“ he went out and won it. He finished it off really well."
Wilkin was quick to joke: "He's already reminded me about three times that he is the one taking the money so I hope he buys me a beer after this."
Wilkin, who is coached by Auckland professional Marcus Wheelhouse, has had a great year where he shot a course record 63 at Lochiel, finished runner-up at the NZ Stroke Play and leading amateur at the Taranaki Energy Open.
"The best thing was I went bogey free today and that was the key to shooting 68 today. I am really pleased that the work I am doing is paying off. It is really rewarding."
Fox, who carded a one under 71 in the final round, rates his mate's chances of building from this performance.
"He is looking to turn pro at the end of the year and I know he wants to push for a spot in the Eisenhower team. It is good to see him finally get rewarded for a good run of form the past couple of months.
"I did remind Fraser that I do get the cheque at least. I am pretty happy where everything is at with my game. There are a lot of things I could have done better but I am going well."
Auckland amateur Sam An shot a three under par 69 in the final round to claim third place, Waikato professional Brad Shilton matched that number to place fourth while defending champion Joshua Munn faded with a two over par 74 to come fifth.
Earlier in the day, Ko created abuzz in the clubhouse when she blitzed the women's field by 17 shots with a course record seven under par 65 in the blustery conditions.
The superstar 15-year-old from the North Shore Golf Club got off to a fast start with a birdie at the second hole, an eagle at the sixth and consecutive birdies on seven and eight to be five under through eight holes.
The birdies dried up until the famous 18th hole at Muriwai where her ball fed off the back slope of the green to set up a birdie chance from 5m.
Ko calmly stepped up and drained the putt across the slope to break the course record she set in round one by two shots.
"It is pretty awesome," said 15-year-old.
"I played well in Singapore and I hoped I would play well here as well and I did so I am happy. I shot better today than the last three days in total so I was happy."
Ko, who has now set or equaled the course record at the West Auckland links three times was happy with how she played the last.
"I hit my second shot a bit big and a bit right but it came down off the bank to the right side of the green so I was pretty happy. Fortunately Munchin [Keh] was next to my ball and was putting first so I got a great line. It was really good.
"I have no idea how much I won by. I felt really confident and I knew that the score difference was quite big so there was no pressure on me.
"Hopefully my course record will stay a bit longer, I seem to play the best here on the windiest days I must be a wind-girl or something."
Ko will play the upcoming North Shore 54 Hole Classic as she prepares to make her major debut when she plays the US Open in early July.
"I am really excited about it. I will be practicing hard for that as it is not a tournament that anyone can play. It is going to be awesome."
Men's Scores after round 4- Sun 6 May 2012
Scores after round 4 - Sun 6 May 2012
273 Fraser Wilkin (Royal Auckland) 70 64 71 68
276 Ryan Fox (P) 69 68 68 71
278 Sam An (Titirangi) 68 72 69 69
279 Brad Shilton (P) 71 69 70 69
281 Joshua Munn (Manawatu) 65 72 70 74
283 Peter Lee (Rotorua) 70 72 69 72
284 Craig Palmer (P) 75 70 73 66
285 Sam Davis (Tauranga) 74 68 72 71, Grant Moorhead (P) 69 72 73 71
286 Michael Hendry (P) 72 69 73 72, Compton Pikari (Te Awamutu) 73 70 69 74
287 Scott Hill (P) 81 70 70 66, Mahal Pearce (P) 75 72 72 68
288 Tom Brockelsby (Royal Wellington) 72 71 73 72
289 Mark Brown (P) 72 77 67 73
290 Ho Jun Sung (St. Andrews) 76 69 74 71, Jared Pender (P) 74 70 72 74, Dean Sipson (P) 71 74 71 74
291 David Klein (P) 77 74 70 70, Nick Gillespie (P) 76 70 72 73, Martin Pettigrew (P) 75 70 71 75, Daniel Graham (Lochiel) 74 69 71 77
292 Brenden Stuart (P) 77 69 75 71, Peter Spearman Burn (P) 69 73 77 73, Mark Purser (P) 70 71 74 77
294 Anthony Cope (North Shore) 77 76 70 71
295 Luke Toomey (Ngaruawahia) 74 76 75 70, Leighton James (P) 73 73 73 76
296 Troy Ropiha (P) 71 80 71 74
Women's Scores after round 4 - Sun 6 May 2012
275 Lydia Ko (North Shore) 67 72 71 65
292 Emily Perry (Lochiel) 73 74 70 75
302 Chantelle Cassidy (Tokoroa) 77 80 70 75
303 Wenyung Keh (Titirangi) 74 73 78 78, Mun Chin Keh (Titirangi) 76 73 76 78
305 Kristin Farrell (Titirangi) 78 75 77 75
311 Larissa Jane Eruera (Akarana) 78 75 80 78
316 Celyn Khoo (Pakuranga) 83 78 76 79, Grace Senior (Tauranga) 76 76 84 80
318 Sarah Bradley (Cambridge) 81 78 76 83
324 Julitta Lam (Muriwai) 81 83 81 79
325 Tyla Kingi (Opotiki) 79 76 89 81
334 Jan Manoonpong (Remuera) 78 86 84 86