The former Tartan Tour No 1, who was sharing the halfway lead in the co-sanctioned European Tour and Challenge Tour event, closed with a one-over 72 in tough conditions for a one-under 283.
Stirling pro Lee finished seven shots behind runaway leader Matt Zions of Australia, who coasted to his first European title with a 69 for 276.
Lee picked up a career-best cheque for 39,571 and moved to third on the Challenge Tour rankings.
"It was always going to be a bit far-fetched to catch Matt, but I'm delighted to finish in a share of second," said Lee. "It's a great achievement and the money will take care of the rest of the season."
Alastair Forsyth shared 12th on 285, while Steven O'Hara (292), Callum Macaulay (293) and Jack Doherty (299) finished down the field.
Zions emulated the sort of dominance being shown by Rory McIlroy in America with a seven-shot victory. With the majority of golf's leading lights trailing in McIlroy's wake at the US Open, it was the perfect opportunity for one of the sport's less celebrated players to shine and Zions took full advantage.
The 32-year-old carded a two-under round of 69 to win by seven strokes from Lee, England's Daniel Denison, Peter Gustafsson of Sweden - the only other three men to finish under par for the tournament.
Denison was one of a group of three just three shots off the lead overnight, but he hit a 73 to fall out of contention, while the other two fared worse, George Coetzee and Federico Colombo carding a 75 and a 76 respectively.
Zions hit a bogey at the par-four fifth but by that time his closest challengers had dropped out and he went on to card four birdies against one further bogey to win with plenty to spare, claiming a first prize of €100,000.
"It feels like I'm dreaming," said Zions. "The last four holes I was wondering when I could start thinking about winning, and when would be too soon that it tempted fate. I had a lump in my throat a couple of times.
"This is a huge day, it's hard to believe. My ball striking was great all week and I hardly missed any greens. We're not out here just to collect the cheque. It was nice to feel those butterflies this morning and feel the adrenaline as I was coming down the stretch. That's why we play. If I was one or two ahead I might've been more nervous. But I tried to treat it like any other round, and on the second I hit a beautiful four iron 220 yards to about 20 feet, so that settled me a lot. I knew it would be tough for the other guys to catch me with low scores in these conditions, so I just tried to be sensible."I'm supposed to be playing French Open qualifying tomorrow but there's no chance I'm going to that now."
Englishman David Dixon's hole in one at the 17th helped him to a 68, the best of the day alongside compatriot Chris Lloyd, with both men finishing among a seven-way tie for 17th.